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Dong X, Zhang T, Gui C, Fei S, Xu H, Chang J, Lian C, Tang W. The critical role of residues Phe120 and Val161 of (2 R,3 R)‑2,3‑butanediol dehydrogenase from Neisseria gonorrhoeae as probed by molecular docking and site-directed mutagenesis. J Basic Microbiol 2024; 64:e2300751. [PMID: 38644586 DOI: 10.1002/jobm.202300751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
NAD+-dependent (2 R,3 R)‑2,3‑butanediol dehydrogenase (BDH) from Neisseria gonorrhoeae (NgBDH) is a representative member of the medium-chain dehydrogenase/reductase (MDR) superfamily. To date, little information is available on the substrate binding sites and catalytic residues of BDHs from this superfamily. In this work, according to molecular docking studies, we found that conserved residues Phe120 and Val161 form strong hydrophobic interactions with both (2 R,3 R)‑2,3‑butanediol (RR-BD) and meso-2,3‑butanediol (meso-BD) and that mutations of these residues to alanine or threonine impair substrate binding. To further evaluate the roles of these two residues, Phe120 and Val161 were mutated to alanine or threonine. Kinetic analysis revealed that, relative to those of wild type, the apparent KM values of the Phe120Ala mutant for RR-BD and meso-BD increased 36- and 369-fold, respectively; the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 586- and 3528-fold, respectively; and the apparent KM values of the Val161Ala mutant for RR-BD and meso-BD increased 4- and 37-fold, respectively, the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 3- and 28-fold, respectively. Additionally, the Val161Thr mutant slightly decreased catalytic efficiencies (twofold with RR-BD; 7.3-fold with meso-BD) due to an increase in KM (sixfold for RR-BD; 24-fold for meso-BD) and a slight increase (2.8-fold with RR-BD; 3.3-fold with meso-BD) in kcat. These findings validate the critical roles of Phe120 and Val161 of NgBDH in substrate binding and catalysis. Overall, the current study provides a better understanding of the substrate binding and catalysis of BDHs within the MDR superfamily.
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Affiliation(s)
- Xue Dong
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Tingting Zhang
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Chuanyue Gui
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Shuping Fei
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Haonan Xu
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Jianrong Chang
- Scientific Research Center, Bengbu Medical University, Bengbu, China
| | - Chaoqun Lian
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Wanggang Tang
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
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2
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Wittmann L, Eigenfeld M, Büchner K, Meiler J, Habisch H, Madl T, Kerpes R, Becker T, Berensmeier S, Schwaminger SP. Millifluidic magnetophoresis-based chip for age-specific fractionation: evaluating the impact of age on metabolomics and gene expression in yeast. LAB ON A CHIP 2024; 24:2987-2998. [PMID: 38739033 DOI: 10.1039/d4lc00185k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
A novel millifluidic process introduces age-based fractionation of S. pastorianus var. carlsbergensis yeast culture through magnetophoresis. Saccharomyces yeast is a model organism for aging research used in various industries. Traditional age-based cell separation methods were labor-intensive, but techniques like magnetic labeling have eased the process by being non-invasive and scalable. Our approach introduces an age-specific fractionation using a 3D-printed millfluidic chip in a two-step process, ensuring efficient cell deflection in the magnetic field and counteracting magnetic induced convection. Among various channel designs, the pinch-shaped channel proved most effective for age differentiation based on magnetically labeled bud scar numbers. Metabolomic analyses revealed changes in certain amino acids and increased NAD+ levels, suggesting metabolic shifts in aging cells. Gene expression studies further underlined these age-related metabolic changes. This innovative platform offers a high-throughput, non-invasive method for age-specific yeast cell fractionation, with potential applications in industries ranging from food and beverages to pharmaceuticals.
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Affiliation(s)
- L Wittmann
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
| | - M Eigenfeld
- TUM School of Life Science, Chair of Brewing and Beverage Technology, Technical University of Munich, Weihenstephaner Steig 20, 85354 Freising, Germany.
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
| | - K Büchner
- TUM School of Life Science, Chair of Brewing and Beverage Technology, Technical University of Munich, Weihenstephaner Steig 20, 85354 Freising, Germany.
| | - J Meiler
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
| | - H Habisch
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
| | - T Madl
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
| | - R Kerpes
- TUM School of Life Science, Chair of Brewing and Beverage Technology, Technical University of Munich, Weihenstephaner Steig 20, 85354 Freising, Germany.
| | - T Becker
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
- Munich Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Lichtenberstr. 4a, 85748 Garching, Germany
| | - S Berensmeier
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
- Munich Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Lichtenberstr. 4a, 85748 Garching, Germany
| | - S P Schwaminger
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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Rohaun SK, Sethu R, Imlay JA. Microbes vary strategically in their metalation of mononuclear enzymes. Proc Natl Acad Sci U S A 2024; 121:e2401738121. [PMID: 38743623 PMCID: PMC11127058 DOI: 10.1073/pnas.2401738121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Studies have determined that nonredox enzymes that are cofactored with Fe(II) are the most oxidant-sensitive targets inside Escherichia coli. These enzymes use Fe(II) cofactors to bind and activate substrates. Because of their solvent exposure, the metal can be accessed and oxidized by reactive oxygen species, thereby inactivating the enzyme. Because these enzymes participate in key physiological processes, the consequences of stress can be severe. Accordingly, when E. coli senses elevated levels of H2O2, it induces both a miniferritin and a manganese importer, enabling the replacement of the iron atom in these enzymes with manganese. Manganese does not react with H2O2 and thereby preserves enzyme activity. In this study, we examined several diverse microbes to identify the metal that they customarily integrate into ribulose-5-phosphate 3-epimerase, a representative of this enzyme family. The anaerobe Bacteroides thetaiotaomicron, like E. coli, uses iron. In contrast, Bacillus subtilis and Lactococcus lactis use manganese, and Saccharomyces cerevisiae uses zinc. The latter organisms are therefore well suited to the oxidizing environments in which they dwell. Similar results were obtained with peptide deformylase, another essential enzyme of the mononuclear class. Strikingly, heterologous expression experiments show that it is the metal pool within the organism, rather than features of the protein itself, that determine which metal is incorporated. Further, regardless of the source organism, each enzyme exhibits highest turnover with iron and lowest turnover with zinc. We infer that the intrinsic catalytic properties of the metal cannot easily be retuned by evolution of the polypeptide.
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Affiliation(s)
| | | | - James A. Imlay
- Department of Microbiology, University of Illinois, Urbana, IL61801
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Jacobi T, Kratzer DA, Plapp BV. Substitution of both histidines in the active site of yeast alcohol dehydrogenase 1 exposes underlying pH dependencies. Chem Biol Interact 2024; 394:110992. [PMID: 38579923 PMCID: PMC11090211 DOI: 10.1016/j.cbi.2024.110992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction. The pH dependencies for several kinetic parameters are shifted from pK values for wild-type ADH of 7.3-8.1 to values for H44R/H48Q ADH of 8.0-9.6, and are assigned to the water or alcohol bound to the catalytic zinc. It appears that the rate of binding of NAD+ is electrostatically favored with zinc-hydroxide whereas binding of NADH is faster with neutral zinc-water. The pH dependencies of catalytic efficiencies (V/EtKm) for ethanol oxidation and acetaldehyde reduction are similarly controlled by deprotonation and protonation, respectively. The substitutions make an enzyme that resembles the homologous horse liver H51Q ADH, which has Arg-47 and Gln-51 and exhibits similar pK values. In the wild-type ADHs, it appears that His-48 (or His-51) in the proton relay systems linked to the catalytic zinc ligands modulate catalytic efficiencies.
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Affiliation(s)
- Tobias Jacobi
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Darla Ann Kratzer
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA.
| | - Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA.
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McDonough R, Williams CC, Hartley CJ, French N, Scott C, Lewis DA. Kinetic Model for the Heterogeneous Biocatalytic Reactions Using Tethered Cofactors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6685-6693. [PMID: 38525517 DOI: 10.1021/acs.langmuir.3c02958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Understanding the mechanism of interfacial enzyme kinetics is critical to the development of synthetic biological systems for the production of value-added chemicals. Here, the interfacial kinetics of the catalysis of β-nicotinamide adenine dinucleotide (NAD+)-dependent enzymes acting on NAD+ tethered to the surface of silica nanoparticles (SiNPs) has been investigated using two complementary and supporting kinetic approaches: enzyme excess and reactant (NAD+) excess. Kinetic models developed for these two approaches characterize several critical reaction steps including reversible enzyme adsorption, complexation, decomplexation, and catalysis of the surface-bound enzyme/NAD+ complex. The analysis reveals a concentrating effect resulting in a very high local concentration of enzyme and cofactor on the particle surface, in which the enzyme is saturated by surface-bound NAD, facilitating a rate enhancement of enzyme/NAD+ complexation and catalysis. This resulted in high enzyme efficiency within the tethered NAD+ system compared to that of the free enzyme/NAD+ system, which increases with decreasing enzyme concentration. The role of enzyme adsorption onto solid substrates with a tethered catalyst (such as NAD+) has potential for creating highly efficient flow biocatalytic systems.
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Affiliation(s)
- Rowan McDonough
- Institute for Nanoscale Science and Technology, School of Chemical and Physical Sciences, Flinders University, Bedford Park, SA 5042, Australia
| | | | | | - Nigel French
- CSIRO Environment, Black Mountain, ACT 2601, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain, ACT 2601, Australia
| | - David A Lewis
- Institute for Nanoscale Science and Technology, School of Chemical and Physical Sciences, Flinders University, Bedford Park, SA 5042, Australia
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Zheng C, Hou S, Zhou Y, Yu C, Li H. Regulation of the PFK1 gene on the interspecies microbial competition behavior of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2024; 108:272. [PMID: 38517486 PMCID: PMC10959778 DOI: 10.1007/s00253-024-13091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
Saccharomyces cerevisiae is a widely used strain for ethanol fermentation; meanwhile, efficient utilization of glucose could effectively promote ethanol production. The PFK1 gene is a key gene for intracellular glucose metabolism in S. cerevisiae. Our previous work suggested that although deletion of the PFK1 gene could confer higher oxidative tolerance to S. cerevisiae cells, the PFK1Δ strain was prone to contamination by other microorganisms. High interspecies microbial competition ability is vital for the growth and survival of microorganisms in co-cultures. The result of our previous studies hinted us a reasonable logic that the EMP (i.e., the Embden-Meyerhof-Parnas pathway, the glycolytic pathway) key gene PFK1 could be involved in regulating interspecies competitiveness of S. cerevisiae through the regulation of glucose utilization and ethanol production efficiency. The results suggest that under 2% and 5% glucose, the PFK1Δ strain showed slower growth than the S288c wild-type and TDH1Δ strains in the lag and exponential growth stages, but realized higher growth in the stationary stage. However, relative high supplement of glucose (10%) eliminated this phenomenon, suggesting the importance of glucose in the regulation of PFK1 in yeast cell growth. Furthermore, during the lag growth phase, the PFK1Δ strain displayed a decelerated glucose consumption rate (P < 0.05). The expression levels of the HXT2, HXT5, and HXT6 genes decreased by approximately 0.5-fold (P < 0.05) and the expression level of the ZWF1 exhibited a onefold increase in the PFK1Δ strain compared to that in the S. cerevisiae S288c wild-type strain (P < 0.05).These findings suggested that the PFK1 inhibited the uptake and utilization of intracellular glucose by yeast cells, resulting in a higher amount of residual glucose in the medium for the PFK1Δ strain to utilize for growth during the reverse overshoot stage in the stationary phase. The results presented here also indicated the potential of ethanol as a defensive weapon against S. cerevisiae. The lower ethanol yield in the early stage of the PFK1Δ strain (P < 0.001) and the decreased expression levels of the PDC5 and PDC6 (P < 0.05), which led to slower growth, resulted in the strain being less competitive than the wild-type strain when co-cultured with Escherichia coli. The lower interspecies competitiveness of the PFK1Δ strain further promoted the growth of co-cultured E. coli, which in turn activated the ethanol production efficiency of the PFK1Δ strain to antagonize it from E. coli at the stationary stage. The results presented clarified the regulation of the PFK1 gene on the growth and interspecies microbial competition behavior of S. cerevisiae and would help us to understand the microbial interactions between S. cerevisiae and other microorganisms. KEY POINTS: • PFK1Δ strain could realize reverse growth overshoot at the stationary stage • PFK1 deletion decreased ethanol yield and interspecific competitiveness • Proportion of E. coli in co-culture affected ethanol yield capacity of yeast cells.
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Affiliation(s)
- Caijuan Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shuxin Hou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yu Zhou
- School of Public Health, Jining Medical University, Jining, 272067, People's Republic of China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Hao Li
- School of Public Health, Jining Medical University, Jining, 272067, People's Republic of China.
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Ma X, Liu Z, Zeng X, Li Z, Luo R, Liu R, Wang C, Gu Y. Genome-Wide Identification and Characterization of the Medium-Chain Dehydrogenase/Reductase Superfamily of Trichosporon asahii and Its Involvement in the Regulation of Fluconazole Resistance. J Fungi (Basel) 2024; 10:123. [PMID: 38392795 PMCID: PMC10889790 DOI: 10.3390/jof10020123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
The medium-chain dehydrogenase/reductase (MDR) superfamily contains many members that are widely present in organisms and play important roles in growth, metabolism, and stress resistance but have not been studied in Trichosporon asahii. In this study, bioinformatics and RNA sequencing methods were used to analyze the MDR superfamily of T. asahii and its regulatory effect on fluconazole resistance. A phylogenetic tree was constructed using Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans, and T. asahii, and 73 MDRs were identified, all of which contained NADPH-binding motifs. T. asahii contained 20 MDRs that were unevenly distributed across six chromosomes. T. asahii MDRs (TaMDRs) had similar 3D structures but varied greatly in their genetic evolution at different phylum levels. RNA-seq and gene expression analyses revealed that the fluconazole-resistant T. asahii strain upregulates xylitol dehydrogenase, and downregulated alcohol dehydrogenase and sorbitol dehydrogenase concluded that the fluconazole-resistant T. asahii strain was less selective toward carbon sources and had higher adaptability to the environment. Overall, our study contributes to our understanding of TaMDRs, providing a basis for further analysis of the genes associated with drug resistance in T. asahii.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiangwen Zeng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhiguo Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Rongyan Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ruiguo Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Chengdu 611800, China
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu 611130, China
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Plapp BV. Solvent isotope and mutagenesis studies on the proton relay system in yeast alcohol dehydrogenase 1. Chem Biol Interact 2024; 388:110853. [PMID: 38151107 PMCID: PMC10843573 DOI: 10.1016/j.cbi.2023.110853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Alcohol dehydrogenase catalyzes the reversible transfer of a hydride directly from an alcohol to the nicotinamide ring of NAD+ to form an aldehyde and NADH, and the proton from the alcohol probably is transferred through a hydrogen-bonded system to the imidazole of His-48. Studies of the pH dependencies, and solvent and substrate isotope effects on the wild-type and the enzyme with His-48 substituted with Gln-48 were used to demonstrate a role for the proton relay system. The H48Q substitution increases affinities for NAD+ and NADH by ∼2-fold, suggesting that the overall protein structure is maintained. In contrast, catalytic efficiencies (V/Km) on ethanol and acetaldehyde and affinity for 2,2,2-trifluoroethanol are decreased by about 10-fold. The pH dependencies for catalytic efficiencies on ethanol and acetaldehyde (log V/Km versus pH), show pK values of about 7.5 for wild-type enzyme, but ethanol oxidation by H48Q ADH is essentially linear over the pH range from 5.5 to 9.2 with a slope of 0.47. Steady-state kinetics and substrate isotope effects suggest that the kinetic mechanism of H48Q ADH has become partly random for oxidation of ethanol. Both wild-type and H48Q ADHs have pH-independent isotope effects for oxidation (V1/Kb) of 1-butanol/1-butanol-d9 of 4, suggesting that hydride transfer is a major rate-limiting step. The pH dependence for butanol oxidation by wild type ADH shows a wavy profile over the pH range from pH 6 to 10, with a ∼2.3-fold larger V1/Kb in D2O than in H2O, an "inverse" isotope effect. The substrate isotope effect of 4 is not altered by the solvent isotope effect, suggesting concerted proton/hydride transfer. The solvent isotope effect can be explained by a ground state with a water bound to the catalytic zinc in the enzyme-NAD+ complex, and a transition state that resembles a complex with NADH and aldehyde. In contrast, the H48Q enzyme has a diminished inverse solvent isotope effect of ∼1.3 and an essentially linear pH dependence with a slope of log V1/Kb against pH of 0.49 for oxidation of 1-butanol, which together are consistent with a transition state where hydroxide ion directly accepts a proton from the 2'-hydroxyl group of the nicotinamide ribose in the proton relay system in the enzyme-NAD+-alcohol complex. The results support a catalytic role for His-48 in the proton relay system.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
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Geng K, Lin Y, Zheng X, Li C, Chen S, Ling H, Yang J, Zhu X, Liang S. Enhanced Expression of Alcohol Dehydrogenase I in Pichia pastoris Reduces the Content of Acetaldehyde in Wines. Microorganisms 2023; 12:38. [PMID: 38257867 PMCID: PMC10820543 DOI: 10.3390/microorganisms12010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Acetaldehyde is an important carbonyl compound commonly detected in wines. A high concentration of acetaldehyde can affect the flavor of wines and result in adverse effects on human health. Alcohol dehydrogenase I (ADH1) in Saccharomyces cerevisiae catalyzes the reduction reaction of acetaldehyde into ethanol in the presence of cofactors, showing the potential to reduce the content of acetaldehyde in wines. In this study, ADH1 was successfully expressed in Pichia pastoris GS115 based on codon optimization. Then, the expression level of ADH1 was enhanced by replacing its promoter with optimized promoters and increasing the copy number of the expression cassette, with ADH1 being purified using nickel column affinity chromatography. The enzymatic activity of purified ADH1 reached 605.44 ± 44.30 U/mg. The results of the effect of ADH1 on the content of acetaldehyde in wine revealed that the acetaldehyde content of wine samples was reduced from 168.05 ± 0.55 to 113.17 ± 6.08 mg/L with the addition of 5 mM NADH and the catalysis of ADH1, and from 135.53 ± 4.08 to 52.89 ± 2.20 mg/L through cofactor regeneration. Our study provides a novel approach to reducing the content of acetaldehyde in wines through enzymatic catalysis.
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Affiliation(s)
- Kun Geng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xueyun Zheng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
- Key Laboratory of Fermentation Engineering of Ministry of Education, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
| | - Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shuting Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - He Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jun Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiangyu Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
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10
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Zheng C, Ji Z, Mathews II, Boxer SG. Enhanced active-site electric field accelerates enzyme catalysis. Nat Chem 2023; 15:1715-1721. [PMID: 37563323 PMCID: PMC10906027 DOI: 10.1038/s41557-023-01287-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023]
Abstract
The design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme's activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn2+ with Co2+. Based on the electric field enhancement, we make a quantitative prediction of rate acceleration-50-fold faster than the wild-type enzyme-which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity-electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.
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Affiliation(s)
- Chu Zheng
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Zhe Ji
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA.
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11
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Borzova VA, Chernikov AM, Mikhaylova VV, Kurganov BI. Change in the Kinetic Regime of Aggregation of Yeast Alcohol Dehydrogenase in the Presence of 2-Hydroxypropyl-β-cyclodextrin. Int J Mol Sci 2023; 24:16140. [PMID: 38003330 PMCID: PMC10671268 DOI: 10.3390/ijms242216140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Chemical chaperones are low-molecular-weight compounds that suppress protein aggregation. They can influence different stages of the aggregation process-the stage of protein denaturation, the nucleation stage and the stage of aggregate growth-and this may lead to a change in the aggregation kinetic regime. Here, the possibility of changing the kinetic regime in the presence of a chemical chaperone 2-hydroxypropyl-β-cyclodextrin (2-HP-β-CD) was investigated for a test system based on the thermally induced aggregation of yeast alcohol dehydrogenase (yADH) at 56 °C. According to differential scanning calorimetry data, 2-HP-β-CD did not affect the stage of the protein molecule unfolding. Dynamic light scattering data indicated changes in the aggregation kinetics of yADH during the nucleation and aggregate growth stages in the presence of the chaperone. The analysis of kinetic curves showed that the order of aggregation with respect to protein (nc), calculated for the stage of aggregate growth, changed from nc = 1 to nc = 2 with the addition of 100 mM 2-HP-β-CD. The mechanism of 2-HP-β-CD action on the yADH thermal aggregation leading to a change in its kinetic regime of aggregation is discussed.
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Affiliation(s)
- Vera A. Borzova
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; (A.M.C.); (V.V.M.)
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12
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Rudzka A, Zdun B, Antos N, Montero LM, Reiter T, Kroutil W, Borowiecki P. Biocatalytic characterization of an alcohol dehydrogenase variant deduced from Lactobacillus kefir in asymmetric hydrogen transfer. Commun Chem 2023; 6:217. [PMID: 37828252 PMCID: PMC10570314 DOI: 10.1038/s42004-023-01013-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Hydrogen transfer biocatalysts to prepare optically pure alcohols are in need, especially when it comes to sterically demanding ketones, whereof the bioreduced products are either essential precursors of pharmaceutically relevant compounds or constitute APIs themselves. In this study, we report on the biocatalytic potential of an anti-Prelog (R)-specific Lactobacillus kefir ADH variant (Lk-ADH-E145F-F147L-Y190C, named Lk-ADH Prince) employed as E. coli/ADH whole-cell biocatalyst and its characterization for stereoselective reduction of prochiral carbonyl substrates. Key enzymatic reaction parameters, including the reaction medium, evaluation of cofactor-dependency, organic co-solvent tolerance, and substrate loading, were determined employing the drug pentoxifylline as a model prochiral ketone. Furthermore, to tap the substrate scope of Lk-ADH Prince in hydrogen transfer reactions, a broad range of 34 carbonylic derivatives was screened. Our data demonstrate that E. coli/Lk-ADH Prince exhibits activity toward a variety of structurally different ketones, furnishing optically active alcohol products at the high conversion of 65-99.9% and in moderate-to-high isolated yields (38-91%) with excellent anti-Prelog (R)-stereoselectivity (up to >99% ee) at substrate concentrations up to 100 mM.
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Affiliation(s)
- Aleksandra Rudzka
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Beata Zdun
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Natalia Antos
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Lia Martínez Montero
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstrasse 28, 8010, Graz, Austria
| | - Tamara Reiter
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstrasse 28, 8010, Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstrasse 28, 8010, Graz, Austria
| | - Paweł Borowiecki
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland.
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13
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Topaloğlu A, Esen Ö, Turanlı-Yıldız B, Arslan M, Çakar ZP. From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications. J Fungi (Basel) 2023; 9:984. [PMID: 37888240 PMCID: PMC10607480 DOI: 10.3390/jof9100984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker's yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology.
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Affiliation(s)
- Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Ömer Esen
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Burcu Turanlı-Yıldız
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Van 65000, Türkiye;
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
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14
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Gutiérrez-Corona JF, González-Hernández GA, Padilla-Guerrero IE, Olmedo-Monfil V, Martínez-Rocha AL, Patiño-Medina JA, Meza-Carmen V, Torres-Guzmán JC. Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential. Cells 2023; 12:2239. [PMID: 37759461 PMCID: PMC10526403 DOI: 10.3390/cells12182239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Fungal alcohol dehydrogenases (ADHs) participate in growth under aerobic or anaerobic conditions, morphogenetic processes, and pathogenesis of diverse fungal genera. These processes are associated with metabolic operation routes related to alcohol, aldehyde, and acid production. The number of ADH enzymes, their metabolic roles, and their functions vary within fungal species. The most studied ADHs are associated with ethanol metabolism, either as fermentative enzymes involved in the production of this alcohol or as oxidative enzymes necessary for the use of ethanol as a carbon source; other enzymes participate in survival under microaerobic conditions. The fast generation of data using genome sequencing provides an excellent opportunity to determine a correlation between the number of ADHs and fungal lifestyle. Therefore, this review aims to summarize the latest knowledge about the importance of ADH enzymes in the physiology and metabolism of fungal cells, as well as their structure, regulation, evolutionary relationships, and biotechnological potential.
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Affiliation(s)
- J. Félix Gutiérrez-Corona
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Gloria Angélica González-Hernández
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Israel Enrique Padilla-Guerrero
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Vianey Olmedo-Monfil
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Ana Lilia Martínez-Rocha
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - J. Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Víctor Meza-Carmen
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Juan Carlos Torres-Guzmán
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
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15
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Plapp BV, Kratzer DA, Souhrada SK, Warth E, Jacobi T. Specific base catalysis by yeast alcohol dehydrogenase I with substitutions of histidine-48 by glutamate or serine residues in the proton relay system. Chem Biol Interact 2023; 382:110558. [PMID: 37247811 PMCID: PMC10527620 DOI: 10.1016/j.cbi.2023.110558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
His-48 in yeast alcohol dehydrogenase I (His 51 in horse liver alcohol dehydrogenase) is a highly conserved residue in the active sites of many alcohol dehydrogenases. The imidazole group of His-48 may participate in base catalysis of proton transfer as it is linked by hydrogen bonds through the 2'-hydroxyl group of the nicotinamide ribose and the hydroxyl group of Thr-45 to the hydroxyl group of the alcohol bound to the catalytic zinc. In this study, His-48 was substituted with a glutamic acid residue to determine if a carboxylate could replace imidazole or to a serine residue to determine if the exposure of the 2'-hydroxyl group of the ribose to solvent would allow proton transfer to water without base catalysis. At pH 7.3, the H48E substitution increases affinity for NAD+ and NADH 17- or 2.6-fold, but decreases catalytic efficiency (V/Km) on ethanol by 70-fold and on acetaldehyde by 6-fold relative to wild-type enzyme. The H48S substitution increases affinity for coenzymes by 2-fold and decreases (V/Km) on ethanol and acetaldehyde only by ∼3-fold. The substituted enzymes show substrate deuterium isotope (H/D) effects of 3-4 for turnover number (V1) and catalytic efficiency (V1/Kb) for ethanol oxidation, indicating that hydrogen transfer is partially rate-limiting and suggesting a somewhat more random mechanism for binding of ethanol and NAD+. For reduction of acetaldehyde, the deuterium isotope effects are small, and the kinetic mechanism appears to be ordered for binding of NADH first and acetaldehyde next. The pH dependencies for H48E and H48S ADHs can be described by a mechanism with pK values of about 6-7 and 9. However, the pH dependencies for oxidation of ethanol and butanol by the H48S enzyme are also simply described by a straight line, with slopes of log V1/Kb against pH of 0.37 or 0.43, respectively. The linear dependence apparently represents catalysis by hydroxide that has a low activity coefficient due to the protein environment, or to a kinetically complex proton transfer. The effects of the substitutions of His-48 show that this residue contributes to catalysis, although many dehydrogenases also have other residues.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Darla Ann Kratzer
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Susan K Souhrada
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Edda Warth
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Tobias Jacobi
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
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16
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Wang R, Liu C, Lyu C, Sun J, Kang C, Ma Y, Wan X, Guo J, Shi L, Wang J, Huang L, Wang S, Guo L. The discovery and characterization of AeHGO in the branching route from shikonin biosynthesis to shikonofuran in Arnebia euchroma. FRONTIERS IN PLANT SCIENCE 2023; 14:1160571. [PMID: 37180378 PMCID: PMC10167036 DOI: 10.3389/fpls.2023.1160571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023]
Abstract
Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon and Arnebia euchroma. Phytochemical studies utilizing both L. erythrorhizon and A. euchroma cultured cells indicate the existence of a competing route branching out from the shikonin biosynthetic pathway to shikonofuran. A previous study has shown that the branch point is the transformation from (Z)-3''-hydroxy-geranylhydroquinone to an aldehyde intermediate (E)-3''-oxo-geranylhydroquinone. However, the gene encoding the oxidoreductase that catalyzes the branch reaction remains unidentified. In this study, we discovered a candidate gene belonging to the cinnamyl alcohol dehydrogenase family, AeHGO, through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines of A. euchroma. In biochemical assays, purified AeHGO protein reversibly oxidized (Z)-3''-hydroxy-geranylhydroquinone to produce (E)-3''-oxo-geranylhydroquinone followed by reversibly reducing (E)-3''-oxo-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters showed that the reduction of (E)-3''-oxo-geranylhydroquinone was stereoselective and efficient in presence of NADPH, which determined that the overall reaction proceeded from (Z)-3''-hydroxy-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone. Considering that there is a competition between the accumulation of shikonin and shikonofuran derivatives in cultured plant cells, AeHGO is supposed to play an important role in the metabolic regulation of the shikonin biosynthetic pathway. Characterization of AeHGO should help expedite the development of metabolic engineering and synthetic biology toward production of shikonin derivatives.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Luqi Huang
- *Correspondence: Luqi Huang, ; Sheng Wang, ; Lanping Guo,
| | - Sheng Wang
- *Correspondence: Luqi Huang, ; Sheng Wang, ; Lanping Guo,
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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17
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Satyaveanthan MV, Ng CL, Awang A, Lam KW, Hassan M. Isolation, purification and biochemical characterization of Conopomorpha cramerella farnesol dehydrogenase. INSECT MOLECULAR BIOLOGY 2023; 32:143-159. [PMID: 36454188 DOI: 10.1111/imb.12820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
In Southeast Asia, Conopomorpha cramerella (Snellen) which is commonly known as the cocoa pod borer (CPB) moth has been identified as the most detrimental pest of Theobroma cacao L. Apart from the various side effects on human health and non-target organisms, heavily relying on synthetic pyrethroid insecticides to control CPB infestations also increases the environmental contamination risks. Thus, developing biorational insecticides that minimally affect the non-target organism and environment by targeting the insect growth regulation process is needed to manage the pest population. In insects, juvenile hormones (JH) regulate critical biological events, especially metamorphosis, development and reproduction. Since the physiological roles of JH III vary among different organisms, the biochemical properties, especially substrate specificity and analogue inhibition, may also be different. Therefore, studies on the JH III biosynthetic pathway enzymes in both plants and insects are beneficial to discover more effective analogues. Bioinformatic analysis and biochemical characterization of a NADP+ -dependent farnesol dehydrogenase, an intermediate enzyme of the JH III pathway, from C. cramerella (CcFolDH), were described in this study. In addition, the farnesol analogues that may act as a potent analogue inhibitor for CcFolDH ware determined using in vitro enzymatic study. The phylogenetic analysis indicated that CcFolDH shared a close phylogenetic relationship to the honeybee's short-chain dehydrogenase/reductase. The 27 kDa CcFolDH has an NADP(H) binding domain with a typical Rossmann fold and is likely a homotetrameric protein in the solution. The enzyme had a greater preference for substrate trans, trans-farnesol and coenzyme NADP+ . In terms of analogue inhibitor inhibition, hexahydroxyfarnesyl acetone showed the highest inhibition (the lowest Ki ) compared to other farnesol analogues. Thus, hexahydroxyfarnesyl acetone would serve as the most potent active ingredient for future biorational pesticide management for C. cramerella infestation. Based on the bioinformatic analyses and biochemical characterizations conducted in this research, we proposed that rCcFolDH differs slightly from other reported farnesol dehydrogenases in terms of molecular weight, substrate preference, coenzymes utilization and analogue inhibitors selection.
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Affiliation(s)
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Alias Awang
- Cocoa Research & Development Centre (Bagan Datuk), Malaysian Cocoa Board, Sg. Sumun, Malaysia
| | - Kok Wai Lam
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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18
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Ruwolt M, He Y, Borges Lima D, Barshop W, Broichhagen J, Huguet R, Viner R, Liu F. Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity. Anal Chem 2023; 95:5248-5255. [PMID: 36926872 PMCID: PMC10061366 DOI: 10.1021/acs.analchem.2c05141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker-modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intact E. coli cells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Yi He
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - William Barshop
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Johannes Broichhagen
- Department of Chemical Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Fan Liu
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany.,Charité─Universitätsmedizin Berlin, Charitépl. 1, Berlin 10117, Germany
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19
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Zhan P, Liu X, Zhang S, Zhu Q, Zhao H, Ren C, Zhang J, Lu L, Cai D, Qin P. Electroenzymatic Reduction of Furfural to Furfuryl Alcohol by an Electron Mediator and Enzyme Orderly Assembled Biocathode. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12855-12863. [PMID: 36859767 DOI: 10.1021/acsami.3c00320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The electroenzymatic valorization of biomass derivatives into valuable biochemicals has a promising outlook. However, bottlenecks including poor electron transfer between the electrode surface and oxidoreductase, inefficient regeneration of cofactors, and high cost of enzymes and electron mediators hindered the realistic applications of the technique. Herein, to address the above technical barriers, a novel bio-electrocatalytic system that integrates the electrochemical NADH regeneration and enzymatic reaction was constructed, using an orderly assembled composite bioelectrode consisting of an outer immobilized enzyme layer and a sandwiched redox mediator rhodium complex layer. The as-prepared composite bioelectrode was further applied for the highly selective hydrogenation of furfural into furfural alcohol. Results indicated that the enzyme activity was significantly improved, while the furfural valorization was promoted by effective interfacial electron transition and co-factor regeneration on the composite bioelectrode. Considerable high furfural conversion (96.4%) can be achieved accompanied by a furfural alcohol selectivity of 90.0% at -1.2 V (vs Ag/AgCl). The novel composite bioelectrode also showed good stability and reusability. Up to 85.1% of the original furfural alcohol selectivity can be preserved after 10 times of recycling. This work presents a promising green alternative for the valorization of furfural, which also shows great potential extending to the valorization of other biomass compounds.
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Affiliation(s)
- Peng Zhan
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xiangshi Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Shiding Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Qian Zhu
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hongqing Zhao
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Cong Ren
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiawen Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Lu Lu
- Paris Curie Engineer School, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Di Cai
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Peiyong Qin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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20
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Romero-Olivares AL, Frey SD, Treseder KK. Tracking fungal species-level responses in soil environments exposed to long-term warming and associated drying. FEMS Microbiol Lett 2023; 370:fnad128. [PMID: 38059856 DOI: 10.1093/femsle/fnad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
Climate change is affecting fungal communities and their function in terrestrial ecosystems. Despite making progress in the understanding of how the fungal community responds to global change drivers in natural ecosystems, little is known on how fungi respond at the species level. Understanding how fungal species respond to global change drivers, such as warming, is critical, as it could reveal adaptation pathways to help us to better understand ecosystem functioning in response to global change. Here, we present a model study to track species-level responses of fungi to warming-and associated drying-in a decade-long global change field experiment; we focused on two free-living saprotrophic fungi which were found in high abundance in our site, Mortierella and Penicillium. Using microbiological isolation techniques, combined with whole genome sequencing of fungal isolates, and community level metatranscriptomics, we investigated transcription-level differences of functional categories and specific genes involved in catabolic processes, cell homeostasis, cell morphogenesis, DNA regulation and organization, and protein biosynthesis. We found that transcription-level responses were mostly species-specific but that under warming, both fungi consistently invested in the transcription of critical genes involved in catabolic processes, cell morphogenesis, and protein biosynthesis, likely allowing them to withstand a decade of chronic stress. Overall, our work supports the idea that fungi that invest in maintaining their catabolic rates and processes while growing and protecting their cells may survive under global climate change.
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Affiliation(s)
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, Unites States
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, United States
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21
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Zavarise A, Sridhar S, Kiema TR, Wierenga RK, Widersten M. Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics. FEBS J 2023; 290:465-481. [PMID: 36002154 PMCID: PMC10087678 DOI: 10.1111/febs.16603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/17/2022] [Accepted: 08/22/2022] [Indexed: 02/05/2023]
Abstract
A group-III iron containing 1,2-propanediol oxidoreductase, FucO, (also known as lactaldehyde reductase) from Escherichia coli was examined regarding its structure-dynamics-function relationships in the catalysis of the NADH-dependent reduction of (2S)-lactaldehyde. Crystal structures of FucO variants in the presence or absence of cofactors have been determined, illustrating large domain movements between the apo and holo enzyme structures. Different structures of FucO variants co-crystallized with NAD+ or NADH together with substrate further suggest dynamic properties of the nicotinamide moiety of the coenzyme that are important for the reaction mechanism. Modelling of the native substrate (2S)-lactaldehyde into the active site can explain the stereoselectivity exhibited by the enzyme, with a critical hydrogen bond interaction between the (2S)-hydroxyl and the side-chain of N151, as well as the previously experimentally demonstrated pro-(R) selectivity in hydride transfer from NADH to the aldehydic carbon. Furthermore, the deuterium kinetic isotope effect of hydride transfer suggests that reduction chemistry is the main rate-limiting step for turnover which is not the case in FucO catalysed alcohol oxidation. We further propose that a water molecule in the active site - hydrogen bonded to a conserved histidine (H267) and the 2'-hydroxyl of the coenzyme ribose - functions as a catalytic proton donor in the protonation of the product alcohol. A hydrogen bond network of water molecules and the side-chains of amino acid residues D360 and H267 links bulk solvent to this proposed catalytic water molecule.
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Affiliation(s)
| | - Shruthi Sridhar
- Department of Chemistry - BMC, Uppsala University, Sweden.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Finland
| | - Tiila-Riikka Kiema
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Finland
| | - Rikkert K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Finland
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22
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Kwolek-Mirek M, Bednarska S, Dubicka-Lisowska A, Maslanka R, Zadrag-Tecza R, Kaszycki P. Unbalance between Pyridine Nucleotide Cofactors in The SOD1 Deficient Yeast Saccharomyces cerevisiae Causes Hypersensitivity to Alcohols and Aldehydes. Int J Mol Sci 2022; 24:ijms24010659. [PMID: 36614102 PMCID: PMC9820918 DOI: 10.3390/ijms24010659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
Alcohol and aldehyde dehydrogenases are especially relevant enzymes involved in metabolic and detoxification reactions that occur in living cells. The comparison between the gene expression, protein content, and enzymatic activities of cytosolic alcohol and aldehyde dehydrogenases of the wild-type strain and the Δsod1 mutant lacking superoxide dismutase 1, which is hypersensitive to alcohols and aldehydes, shows that the activity of these enzymes is significantly higher in the Δsod1 mutant, but this is not a mere consequence of differences in the enzymatic protein content nor in the expression levels of genes. The analysis of the NAD(H) and NADP(H) content showed that the higher activity of alcohol and aldehyde dehydrogenases in the Δsod1 mutant could be a result of the increased availability of pyridine nucleotide cofactors. The higher level of NAD+ in the Δsod1 mutant is not related to the higher level of tryptophan; in turn, a higher generation of NADPH is associated with the upregulation of the pentose phosphate pathway. It is concluded that the increased sensitivity of the Δsod1 mutant to alcohols and aldehydes is not only a result of the disorder of redox homeostasis caused by the induction of oxidative stress but also a consequence of the unbalance between pyridine nucleotide cofactors.
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Affiliation(s)
- Magdalena Kwolek-Mirek
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.K.-M.); (R.Z.-T.); Tel.: +48-17-785-5412 (M.K.-M.); +48-17-785-5413 (R.Z.-T.)
| | - Sabina Bednarska
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Aleksandra Dubicka-Lisowska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
| | - Roman Maslanka
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.K.-M.); (R.Z.-T.); Tel.: +48-17-785-5412 (M.K.-M.); +48-17-785-5413 (R.Z.-T.)
| | - Pawel Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
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23
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Bisht N, Dalal V, Tewari L. Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm. J Biomol Struct Dyn 2022; 40:12022-12036. [PMID: 34424128 DOI: 10.1080/07391102.2021.1967196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C6/C5 co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of -4.55 and -4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein-ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein-ligand complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Bisht
- Department of Microbiology, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lakshmi Tewari
- Department of Microbiology, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
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24
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Langley C, Tatsis E, Hong B, Nakamura Y, Paetz C, Stevenson CEM, Basquin J, Lawson DM, Caputi L, O'Connor SE. Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism. Angew Chem Int Ed Engl 2022; 61:e202210934. [PMID: 36198083 PMCID: PMC9828224 DOI: 10.1002/anie.202210934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/19/2022]
Abstract
Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.
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Affiliation(s)
- Chloe Langley
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Evangelos Tatsis
- Chinese Academy of Sciences Centre for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and Ecology300 Feng Lin RoadShanghai200032China
| | - Benke Hong
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Yoko Nakamura
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany,Research Group Biosynthesis and NMRMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Christian Paetz
- Research Group Biosynthesis and NMRMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Clare E. M. Stevenson
- Department of Biochemistry and MetabolismJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Jerome Basquin
- Department of Structural Cell BiologyMax-Planck Institute for BiochemistryAm Klopferspitz 18, Martinsried82152PlaneggGermany
| | - David M. Lawson
- Department of Biochemistry and MetabolismJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Lorenzo Caputi
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Sarah E. O'Connor
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
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25
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Liu L, Zhao PT, Hu CY, Tian D, Deng H, Meng YH. Screening low-methanol and high-aroma produced yeasts for cider fermentation by transcriptive characterization. Front Microbiol 2022; 13:1042613. [PMID: 36439849 PMCID: PMC9691974 DOI: 10.3389/fmicb.2022.1042613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/27/2022] [Indexed: 11/12/2022] Open
Abstract
The commercial active dry yeast strains used for cider production in China are far behind the requirements of the cider industry development in recent decades. In this study, eight yeasts, including Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia bruneiensis, and Pichia kudriavzevii, were screened and assessed by growth performance, methanol production, aroma analysis, and their transcriptive characterization. Saccharomyces cerevisiae strains WFC-SC-071 and WFC-SC-072 were identified as promising alternatives for cider production. Strains WFC-SC-071 and WFC-SC-072 showed an excellent growth capacity characterized by 91.6 and 88.8% sugar utilization, respectively. Methanol production by both strains was below 200 mg/L. Key aroma compounds imparting cider appreciably characteristic aroma increased in cider fermented by strains WFC-SC-071 and WFC-SC-072. RT-qPCR analysis suggested that most genes associated with growth capacity, carbohydrate uptake, and aroma production were upregulated in WFC-SC-071 and WFC-SC-072. Overall, two Saccharomyces cerevisiae strains are the optimal starters for cider production to enable the diversification of cider, satisfy the differences in consumer demand, and promote cider industry development.
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Affiliation(s)
- Liang Liu
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
| | - Peng Tao Zhao
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
| | - Ching Yuan Hu
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, Honolulu, HI, United States
| | - Dan Tian
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
| | - Hong Deng
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
- *Correspondence: Hong Deng,
| | - Yong Hong Meng
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
- Yong Hong Meng,
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26
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Quenching of Protein Fluorescence by Fullerenol C 60(OH) 36 Nanoparticles. Int J Mol Sci 2022; 23:ijms232012382. [PMID: 36293241 PMCID: PMC9603995 DOI: 10.3390/ijms232012382] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
The effect of the interaction between fullerenol C60(OH)36 (FUL) and alcohol dehydrogenase (ADH) from Saccharomyces cerevisiae and human serum albumin (HSA) was studied by absorption spectroscopy, fluorescence spectroscopy, and time-resolved fluorescence spectroscopy. As shown in the study, the fluorescence intensities of ADH and HSA at excitation wavelengths λex = 280 nm (Trp, Tyr) and λex = 295 nm (Trp) are decreased with the increase in the FUL concentration. The results of time-resolved measurements indicate that both quenching mechanisms, dynamic and static, are present. The binding constant Kb and the number of binding sites were obtained for HSA and ADH. Thus, the results indicated the formation of FUL complexes and proteins. However, the binding of FUL to HSA is much stronger than that of ADH. The transfer of energy from the protein to FUL was also proved.
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27
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Plapp BV, Gakhar L, Subramanian R. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Acta Crystallogr D Struct Biol 2022; 78:1221-1234. [PMID: 36189742 PMCID: PMC9527765 DOI: 10.1107/s2059798322008361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD+ and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å2) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å2 for the overall complexes and of 5-10 Å2 for C4N of NAD+ and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD+ and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.
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Affiliation(s)
- Bryce V. Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
| | - Lokesh Gakhar
- Protein and Crystallography Facility, Carver College of Medicine, The University of Iowa, Iowa City, IA 52252, USA
| | - Ramaswamy Subramanian
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
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28
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Sherry Wines: Worldwide Production, Chemical Composition and Screening Conception for Flor Yeasts. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The manufacturing of sherry wines is a unique, carefully regulated process, from harvesting to quality control of the finished product, involving dynamic biological aging in a “criadera-solera” system or some other techniques. Specialized “flor” strains of the yeast Saccharomyces cerevisiae play the central role in the sherry manufacturing process. As a result, sherry wines have a characteristic and unique chemical composition that determines their organoleptic properties (such as color, odor, and taste) and distinguishes them from all other types of wine. The use of modern methods of genetics and biotechnology contributes to a deep understanding of the microbiology of sherry production and allows us to define a new methodology for breeding valuable flor strains. This review discusses the main sherry-producing regions and the chemical composition of sherry wines, as well as genetic, oenological, and other selective markers for flor strains that can be used for screening novel candidates that are promising for sherry production among environmental isolates.
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29
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Dinh T, Rahn KT, Phillips RS. Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from
Thermoanaerobacter pseudoethanolicus
reveal the dynamics of ligand exchange and the proton relay network. Proteins 2022; 90:1570-1583. [DOI: 10.1002/prot.26339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tung Dinh
- Department of Chemistry University of Georgia Athens Georgia USA
| | - K. Troy Rahn
- Department of Chemistry University of Georgia Athens Georgia USA
| | - Robert S. Phillips
- Department of Chemistry University of Georgia Athens Georgia USA
- Department of Biochemistry and Molecular Biology University of Georgia Athens Georgia USA
- Center for Metalloenzyme Studies University of Georgia Athens Georgia USA
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30
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Inhibition mechanism of baicalein against alcohol dehydrogenase in vitro via biological techniques, spectroscopy and computer simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Pietricola G, Chamorro L, Castellino M, Maureira D, Tommasi T, Hernández S, Wilson L, Fino D, Ottone C. Covalent Immobilization of Dehydrogenases on Carbon Felt for Reusable Anodes with Effective Electrochemical Cofactor Regeneration. Chemistry 2022; 11:e202200102. [PMID: 35856864 PMCID: PMC9630042 DOI: 10.1002/open.202200102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/17/2022] [Indexed: 01/31/2023]
Abstract
This study presents the immobilization with aldehyde groups (glyoxyl carbon felt) of alcohol dehydrogenase (ADH) and formate dehydrogenase (FDH) on carbon-felt-based electrodes. The compatibility of the immobilization method with the electrochemical application was studied with the ADH bioelectrode. The electrochemical regeneration process of nicotinamide adenine dinucleotide in its oxidized form (NAD+ ), on a carbon felt surface, has been deeply studied with tests performed at different electrical potentials. By applying a potential of 0.4 V versus Ag/AgCl electrode, a good compromise between NAD+ regeneration and energy consumption was observed. The effectiveness of the regeneration of NAD+ was confirmed by electrochemical oxidation of ethanol catalyzed by ADH in the presence of NADH, which is the no active form of the cofactor for this reaction. Good reusability was observed by using ADH immobilized on glyoxyl functionalized carbon felt with a residual activity higher than 60 % after 3 batches.
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Affiliation(s)
- Giuseppe Pietricola
- Department of Applied Science and TechnologyPolitecnico di TorinoCorso Duca degli Abruzzi 2410129TurinItaly
| | - Lesly Chamorro
- Escuela de Ingeniería BioquímicaPontificia Universidad Católica de ValparaísoAvenida Brasil 2085ValparaísoChile
| | - Micaela Castellino
- Department of Applied Science and TechnologyPolitecnico di TorinoCorso Duca degli Abruzzi 2410129TurinItaly
| | - Diego Maureira
- Escuela de Ingeniería BioquímicaPontificia Universidad Católica de ValparaísoAvenida Brasil 2085ValparaísoChile
| | - Tonia Tommasi
- Department of Applied Science and TechnologyPolitecnico di TorinoCorso Duca degli Abruzzi 2410129TurinItaly
| | - Simelys Hernández
- Department of Applied Science and TechnologyPolitecnico di TorinoCorso Duca degli Abruzzi 2410129TurinItaly
| | - Lorena Wilson
- Escuela de Ingeniería BioquímicaPontificia Universidad Católica de ValparaísoAvenida Brasil 2085ValparaísoChile
| | - Debora Fino
- Department of Applied Science and TechnologyPolitecnico di TorinoCorso Duca degli Abruzzi 2410129TurinItaly
| | - Carminna Ottone
- Escuela de Ingeniería BioquímicaPontificia Universidad Católica de ValparaísoAvenida Brasil 2085ValparaísoChile
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32
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Zhu W, Wang Y, Lv L, Wang H, Shi W, Liu Z, Yang W, Zhu J, Lu H. SHTXTHHly, an extracellular secretion platform for the preparation of bioactive peptides and proteins in Escherichia coli. Microb Cell Fact 2022; 21:128. [PMID: 35761329 PMCID: PMC9235172 DOI: 10.1186/s12934-022-01856-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background In previous work, we developed an E. coli extracellular secretion platform XTHHly based on the hemolysin A secretion system. It can produce bioactive peptides with simple purification procedures. However, the wider application of this platform is limited by poor secretion efficiency. Results In this study, we first discovered a positive correlation between the isoelectric point (pI) value of the target protein and the secretion level of the XTHHly system. Given the extremely high secretion level of S tag, we fused it at the N-terminus and created a novel SHTXTHHly system. The SHTXTHHly system significantly increased the secretion levels of antimicrobial peptides (PEW300, LL37, and Aurein 1.2) with full bioactivities, suggesting its excellent capacity for secretory production of bioactive peptides. Furthermore, RGDS, IL-15, and alcohol dehydrogenase were successfully secreted, and their bioactivities were largely maintained in the fusion proteins, indicating the potential applications of the novel system for the rapid determination of protein bioactivities. Finally, using the SHTXTHHly system, we produced the monomeric Fc, which showed a high affinity for Fcγ Receptor I and mediated the antibody-dependent immunological effects of immune cells, demonstrating its potential applications in immunotherapies. Conclusions The SHTXTHHly system described here facilitates the secretory production of various types of proteins in E. coli. In comparison to previously reported expression systems, our work enlightens an efficient and cost-effective way to evaluate the bioactivities of target proteins or produce them. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01856-8.
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Affiliation(s)
- Wen Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Liangyin Lv
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wenqiang Shi
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zexin Liu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wei Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huili Lu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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Iitani K, Nakaya M, Tomono T, Toma K, Arakawa T, Tsuchido Y, Mitsubayashi K, Takeda N. Enzyme-embedded electrospun fiber sensor of hydrophilic polymer for fluorometric ethanol gas imaging in vapor phase. Biosens Bioelectron 2022; 213:114453. [PMID: 35728364 DOI: 10.1016/j.bios.2022.114453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
Non-invasive measurement of volatile organic compounds (VOCs) emitted from living organisms is a powerful technique for diagnosing health conditions or diseases in humans. Bio-based gas sensors are suitable for the sensitive and selective measurement of a target VOC from a complex mixture of VOCs. Conventional bio-based sensors are normally prepared as wet-type probes to maintain proteins such as enzymes in a stable state, resulting in limitations in the commercialization of sensors, their operating environment, and performance. In this study, we present an enzyme-based fluorometric electrospun fiber sensor (eFES) mesh as a gas-phase biosensor in dry form. The eFES mesh targeting ethanol was fabricated by simple one-step electrospinning of polyvinyl alcohol with an alcohol dehydrogenase and an oxidized form of nicotinamide adenine dinucleotide. The enzyme embedded in the eFES mesh worked actively in a dry state without pretreatment. Substrate specificity was also maintained, and the sensor responded well to ethanol with a sufficient dynamic range. Adjustment of the pH and coenzyme quantity in the eFES mesh also affected enzyme activity. The dry-form biosensor-eFES mesh-will open a new direction for gas-phase biosensors because of its remarkable performance and simple fabrication, which is advantageous for commercialization.
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Affiliation(s)
- Kenta Iitani
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan; Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Misa Nakaya
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Tsubomi Tomono
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Koji Toma
- Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Takahiro Arakawa
- Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Yuji Tsuchido
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kohji Mitsubayashi
- Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan; Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Naoya Takeda
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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Pinto J, Chadha A, Gummadi SN. Purification and characterisation of (S)-specific alcohol dehydrogenase from Candida parapsilosis ATCC 7330. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Insight into the binding characteristics of rutin and alcohol dehydrogenase: Based on the biochemical method, spectroscopic experimental and molecular model. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 228:112394. [PMID: 35086025 DOI: 10.1016/j.jphotobiol.2022.112394] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 12/19/2022]
Abstract
Alcohol dehydrogenase (ADH) is a crucial enzyme in the alcohol metabolism pathway. Its activity is associated with the development of alcohol-relative diseases. Rutin is a kind of widely distributed dietary flavonoids, which have the ability to resist alcohol-induced liver injury. Here, the role of rutin on alcohol metabolism was investigated via the methods of biochemistry, spectroscopy and computer simulation. The experiment results demonstrated that rutin entered into the position of coenzyme (NAD) on ADH and formed a binary complex, which of process activated the catalyze activity of ADH in a concentration dependent manner. The combination of rutin on ADH induced microenvironmental variations as well as secondary structural change of ADH, where the level of α-helix reduced yet β-sheet raised. The values of ∆H and ∆S suggested that H-bonds and van der Waals force occupied vital roles in the stabilization of ADH-rutin complex. Furthermore, molecular docking results further confirmed that the H-bonds between the hydroxyl groups on the benzene rings of rutin and surrounding amino acid were beneficial to maintain the stability of complex. Particularly, the van der Waals force and π-alkyl between rutin and Val residues may be the main reason for activation of ADH activity.
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Antonopoulou I, Rova U, Christakopoulos P. CO 2 to Methanol: A Highly Efficient Enzyme Cascade. Methods Mol Biol 2022; 2487:317-344. [PMID: 35687244 DOI: 10.1007/978-1-0716-2269-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Carbon dioxide (CO2) has been increasingly regarded not only as a greenhouse gas but also as a valuable feedstock for carbon-based chemicals. In particular, biological approaches have drawn attention as models for the production of value-added products, as CO2 conversion serves many natural processes. Enzymatic CO2 reduction in vitro is a very promising route to produce fossil free and bio-based fuel alternatives, such as methanol. In this chapter, the advances in constructing competitive multi-enzymatic systems for the reduction of CO2 to methanol are discussed. Different integrated methods are presented, aiming to address technological challenges, such as the cost effectiveness, need for material regeneration and reuse and improving product yields of the process.
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Affiliation(s)
- Io Antonopoulou
- Biochemical Process Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| | - Ulrika Rova
- Biochemical Process Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
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Das PK, Mishra A. Thermodynamics of Multilayer Protein Adsorption on Gold Nanoparticle Surface. Phys Chem Chem Phys 2022; 24:22464-22476. [DOI: 10.1039/d2cp02439j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the thermodynamics of protein adsorption on negatively charged colloidal gold nanoparticles (GNPs) of 16 nm to 69 nm at pH 7.0. Three biologically important proteins of varying size,...
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Abstract
Fossil fuels are a major contributor to climate change, and as the demand for energy production increases, alternative sources (e.g., renewables) are becoming more attractive. Biofuels such as bioethanol reduce reliance on fossil fuels and can be compatible with the existing fleet of internal combustion engines. Incorporation of biofuels can reduce internal combustion engine (ICE) fleet carbon dioxide emissions. Bioethanol is typically produced via microbial fermentation of fermentable sugars, such as glucose, to ethanol. Traditional feedstocks (e.g., first-generation feedstock) include cereal grains, sugar cane, and sugar beets. However, due to concerns regarding food sustainability, lignocellulosic (second-generation) and algal biomass (third-generation) feedstocks have been investigated. Ethanol yield from fermentation is dependent on a multitude of factors. This review compares bioethanol production from a range of feedstocks, and elaborates on available technologies, including fermentation practices. The importance of maintaining nutrient homeostasis of yeast is also examined. The purpose of this review is to provide industrial producers and policy makers insight into available technologies, yields of bioethanol achieved by current manufacturing practices, and goals for future innovation.
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Pal S, Plapp BV. The Thr45Gly substitution in yeast alcohol dehydrogenase substantially decreases catalysis, alters pH dependencies, and disrupts the proton relay system. Chem Biol Interact 2021; 349:109650. [PMID: 34529977 PMCID: PMC8530938 DOI: 10.1016/j.cbi.2021.109650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
X-Ray crystallography shows that the hydroxyl group of Thr-45 in the fermentative alcohol dehydrogenase (ADH1) from Saccharomyces cerevisiae is hydrogen-bonded to the hydroxyl group of the alcohol bound to the catalytic zinc and is part of a proton relay system linked to His-48. The contribution of Thr-45 to catalysis was studied with steady state kinetics of the enzyme with the T45G substitution. Affinities for coenzymes decrease by only 2-4-fold, but the turnover numbers (V/Et) and catalytic efficiencies (V/KmEt) decrease 480-fold and 2900-fold for the oxidation of ethanol and 450-fold and 8400-fold for acetaldehyde reduction, respectively, relative to wild-type enzyme. Binding of NADH appears to require protonation of a group with a pK value of ∼7.4 in wild-type ADH1, but the pK value for T45G ADH1 appears to be less than 5. For wild-type enzyme, the pH dependencies for ethanol oxidation (V1/Et and V1/KbEt) are maximal above pK values of 7.0-7.7 and are attributed to the ionization of the alcohol or water bound to the catalytic zinc facilitated by His-48 in the enzyme-NAD+ complexes. For T45G ADH1, these pK values are shifted to 6.3. The reduction of acetaldehyde (V2/Et and V2/KpEt) modestly increases as the pH increases for wild-type and T45G enzymes. The removal of the hydroxyethyl group of Thr-45 disrupts the connection of the oxygen of ligands bound to the catalytic zinc with the proton relay system and formation of productive catalytic states. The conformational change of the enzyme and the exchange of ligands on the catalytic zinc can also be affected. Assignments of groups responsible for the pK values are discussed in the context of studies on other forms of horse liver and yeast ADHs. The substitutions with Ala-45 and Cys-45 in yeast ADH1 and the homologous substitutions with Ala-48 in horse and human liver ADHs also significantly decrease catalytic efficiency. Threonine or serine residues at this position in alcohol dehydrogenases are highly conserved and contribute substantially to catalysis.
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Affiliation(s)
- Suresh Pal
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52246, USA
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52246, USA.
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Serleti A, Xiao X, Shortall K, Magner E. Use of Self‐Assembled Monolayers for the Sequential and Independent Immobilisation of Enzymes. ChemElectroChem 2021. [DOI: 10.1002/celc.202101145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Alessandro Serleti
- Department of Chemical Sciences Bernal Institute University of Limerick Limerick Ireland
| | - Xinxin Xiao
- Department of Chemistry Technical University of Denmark Kongens Lyngby 2800 Denmark
| | - Kim Shortall
- Department of Chemical Sciences Bernal Institute University of Limerick Limerick Ireland
| | - Edmond Magner
- Department of Chemical Sciences Synthesis and Solid State Pharmaceutical Research Centre Bernal Institute MS1016, University of Limerick Limerick Ireland
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Meena J, Gupta A, Ahuja R, Singh M, Panda AK. Recent advances in nano-engineered approaches used for enzyme immobilization with enhanced activity. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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42
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Expression, purification and X-ray crystal diffraction analysis of alcohol dehydrogenase 1 from Artemisia annua L. Protein Expr Purif 2021; 187:105943. [PMID: 34273542 DOI: 10.1016/j.pep.2021.105943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/30/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022]
Abstract
Alcohol dehydrogenase 1 identified from Artemisia annua (AaADH1) is a 40 kDa protein that predominately expressed in young leaves and buds, and catalyzes dehydrogenation of artemisinic alcohol to artemisinic aldehyde in artemisinin biosynthetic pathway. In this study, AaADH1 encoding gene was subcloned into vector pET-21a(+) and expressed in Escherichia coli. BL21(DE3), and purified by Co2+ affinity chromatography. Anion exchange chromatography was performed until the protein purity reached more than 90%. Crystallization of AaADH1 was conducted for further investigation of the molecular mechanism of catalysis, and hanging-drop vapour diffusion method was used in experiments. The results showed that the apo AaADH1 crystal diffracted to 2.95 Å resolution, and belongs to space group P1, with unit-cell parameters, a = 77.53 Å, b = 78.49 Å, c = 102.44 Å, α = 71.88°, β = 74.02°, γ = 59.97°. The crystallization condition consists of 0.1 M Bis-Tris pH 6.0, 13% (w/v) PEG 8000 and 5% (v/v) glycerol.
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43
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Adebami GE, Kuila A, Ajunwa OM, Fasiku SA, Asemoloye MD. Genetics and metabolic engineering of yeast strains for efficient ethanol production. J FOOD PROCESS ENG 2021. [DOI: 10.1111/jfpe.13798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Arindam Kuila
- Department of Bioscience and Biotechnology Banasthali University Vanasthali India
| | - Obinna M. Ajunwa
- Department of Microbiology Modibbo Adama University of Technology Yola Nigeria
| | - Samuel A. Fasiku
- Department of Biological Sciences Ajayi Crowther University Oyo Nigeria
| | - Michael D. Asemoloye
- Department of Pharmaceutical Science and Technology Tianjin University Tianjin China
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Hayashi S, Kuramata M, Abe T, Yamaguchi N, Takagi H, Tanikawa H, Iino M, Sugimoto K, Ishikawa S. Deficiency in alcohol dehydrogenase 2 reduces arsenic in rice grains by suppressing silicate transporters. PLANT PHYSIOLOGY 2021; 186:611-623. [PMID: 33620496 PMCID: PMC8154085 DOI: 10.1093/plphys/kiab086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 05/14/2023]
Abstract
Paddy fields are anaerobic and facilitate arsenite (As(III)) elution from the soil. Paddy-field rice accumulates arsenic (As) in its grains because silicate transporters actively assimilate As(III) during the reproductive stage. Reducing the As level in rice grains is an important challenge for agriculture. Using a forward genetic approach, we isolated a rice (Oryza sativa) mutant, low arsenic line 3 (las3), whose As levels were decreased in aerial tissues, including grains. The low-As phenotype was not observed in young plants before heading (emergence of the panicle). Genetic analyses revealed that a deficiency in alcohol dehydrogenase (ADH) 2 by mutation is responsible for the phenotype. Among the three rice ADH paralogues, ADH2 was the most efficiently produced in root tissue under anaerobic conditions. In wild-type (WT), silicon and As concentrations in aerial tissues increased with growth. However, the increase was suppressed in las3 during the reproductive stage. Accordingly, the gene expression of two silicate transporters, Lsi1 and Lsi2, was increased in WT around the time of heading, whereas the increase was suppressed in las3. These results indicate that the low-As phenotype in las3 is due to silicate transporter suppression. Measurement of intracellular pH by 31P-nuclear magnetic resonance revealed intracellular acidification of las3 roots under hypoxia, suggesting that silicate transporter suppression in las3 might arise from an intracellular pH decrease, which is known to be facilitated by a deficiency in ADH activity under anaerobic conditions. This study provides valuable insight into reducing As levels in rice grains.
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Affiliation(s)
- Shimpei Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Tadashi Abe
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Noriko Yamaguchi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Hiroki Takagi
- Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Manaka Iino
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
- Author for communication:
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45
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Arsalan A, Hashmi MA, Zofair SFF, Ahmad S, Khan MA, Younus H. Activation of yeast alcohol dehydrogenase in the presence of citrate stabilized gold nanoparticles: An insight into its interaction and modulation mechanism. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Satyaveanthan MV, Suhaimi SA, Ng CL, Muhd-Noor ND, Awang A, Lam KW, Hassan M. Purification, biochemical characterisation and bioinformatic analysis of recombinant farnesol dehydrogenase from Theobroma cacao. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:143-155. [PMID: 33588320 DOI: 10.1016/j.plaphy.2021.01.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
The juvenile hormones (JH) in plants are suggested to act as a form of plant defensive strategy especially against insect herbivory. The oxidation of farnesol to farnesoic acid is a key step in the juvenile hormone biosynthesis pathway. We herein present the purification and characterisation of the recombinant Theobroma cacao farnesol dehydrogenase enzyme that catalyses oxidation of farnesol to farnesal. The recombinant enzyme was purified to apparent homogeneity by affinity chromatography. The purified enzyme was characterised in terms of its deduced amino acid sequences, phylogeny, substrate specificity, kinetic parameters, structural modeling, and docking simulation. The phylogenetic analysis indicated that the T. cacao farnesol dehydrogenase (TcFolDH) showed a close relationship with A. thaliana farnesol dehydrogenase gene. The TcFolDH monomer had a large N-terminal domain which adopted a typical Rossmann-fold, harboring the GxxGxG motif (NADP(H)-binding domain) and a small C-terminal domain. The enzyme was a homotrimer comprised of subunits with molecular masses of 36 kDa. The TcFolDH was highly specific to NADP+ as coenzyme. The substrate specificity studies showed trans, trans-farnesol was the most preferred substrate for the TcFolDH, suggesting that the purified enzyme was a NADP+-dependent farnesol dehydrogenase. The docking of trans, trans-farnesol and NADP+ into the active site of the enzyme showed the important residues, and their interactions involved in the substrate and coenzyme binding of TcFolDH. Considering the extensive involvement of JH in both insects and plants, an in-depth knowledge on the recombinant production of intermediate enzymes of the JH biosynthesis pathway could help provide a potential method for insect control.
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Affiliation(s)
| | - Saidi-Adha Suhaimi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia
| | - Noor-Dina Muhd-Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia; Enzyme & Microbial Technology Center (EMTech), Faculty of Biotechnology & Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, 43400, Malaysia
| | - Alias Awang
- Cocoa Research & Development Centre (Bagan Datuk), Malaysian Cocoa Board, P.O. Box 30, Sg. Dulang Road, Sg. Sumun, Perak, 36307, Malaysia
| | - Kok Wai Lam
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia.
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Wilcox XE, Chung CB, Slade KM. Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase. Biochem Biophys Rep 2021; 26:100956. [PMID: 33665382 PMCID: PMC7905371 DOI: 10.1016/j.bbrep.2021.100956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/03/2021] [Accepted: 02/09/2021] [Indexed: 12/01/2022] Open
Abstract
In order to better understand how the complex, densely packed, heterogeneous milieu of a cell influences enzyme kinetics, we exposed opposing reactions catalyzed by yeast alcohol dehydrogenase (YADH) to both synthetic and protein crowders ranging from 10 to 550 kDa. The results reveal that the effects from macromolecular crowding depend on the direction of the reaction. The presence of the synthetic polymers, Ficoll and dextran, decrease Vmax and Km for ethanol oxidation. In contrast, these crowders have little effect or even increase these kinetic parameters for acetaldehyde reduction. This increase in Vmax is likely due to excluded volume effects, which are partially counteracted by viscosity hindering release of the NAD+ product. Macromolecular crowding is further complicated by the presence of a depletion layer in solutions of dextran larger than YADH, which diminishes the hindrance from viscosity. The disparate effects from 25 g/L dextran or glucose compared to 25 g/L Ficoll or sucrose reveals that soft interactions must also be considered. Data from binary mixtures of glucose, dextran, and Ficoll support this “tuning” of opposing factors. While macromolecular crowding was originally proposed to influence proteins mainly through excluded volume effects, this work compliments the growing body of evidence revealing that other factors, such as preferential hydration, chemical interactions, and the presence of a depletion layer also contribute to the overall effect of crowding. Yeast alcohol dehydrogenase reduction of acetaldehyde is enhanced by crowding. Crowding effects on YADH kinetics depend on the direction of the reaction. Crowders like dextran can be used as a tool to elucidate enzyme mechanism. Excluded volume optimizes YADH hydride transfer; viscosity hinders product release. The presence of a depletion layer with large crowders mitigates their effects.
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Affiliation(s)
- Xander E Wilcox
- Department of Chemistry, University of California at Davis, CA, 95616, USA
| | - Charmaine B Chung
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
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48
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Xu L, Wang LC, Su BM, Xu XQ, Lin J. Efficient biosynthesis of (2S, 3R)-4-methylsulfonylphenylserine by artificial self-assembly of enzyme complex combined with an intensified acetaldehyde elimination system. Bioorg Chem 2021; 110:104766. [PMID: 33662895 DOI: 10.1016/j.bioorg.2021.104766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 01/13/2023]
Abstract
(2S, 3R)-4-methylsulfonylphenylserine [(2S, 3R)-MPS], a key chiral precursor for antibiotics florfenicol and thiamphenicol, could be asymmetrically synthesized by l-threonine transaldolase (LTTA) coupled with an acetaldehyde elimination system. The low efficiency of acetaldehyde elimination system blocked further accumulation of (2S, 3R)-MPS. To address this issue, strengthening acetaldehyde elimination system and enzyme self-assembly strategy were combined to accelerate biosynthesis of (2S, 3R)-MPS. The new multi-enzyme cascade with intensified acetaldehyde elimination system BL21 (PsLTTAD2/ScADH/BtGDH) could produce (2S, 3R)-MPS with a titer of 157.6 mM, 1.7-folds than that produced by the original system BL21 (PsLTTAD2/ApADH/CbFDH). Moreover, self-assembly of PsLTTAD2 and ScADH by respective fusion of SpyTag and SpyCatcher were carried out to develop a self-assembled multi-enzyme cascade BL21 (ST-PsLTTAD2/SC-ScADH/BtGDH). As a result, the yield of (2S, 3R)-MPS was up to 248.1 mM with 95% de. As far as we knew, that represented the highest yield of (2S, 3R)-MPS by enzymatic synthesis, and therefore was a promising and green route for industrial production of this valuable compound.
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Affiliation(s)
- Lian Xu
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
| | - Li-Chao Wang
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
| | - Bing-Mei Su
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
| | - Xin-Qi Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Juan Lin
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China.
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49
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Guntupalli SR, Li Z, Chang L, Plapp BV, Subramanian R. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry 2021; 60:663-677. [PMID: 33620215 DOI: 10.1021/acs.biochem.0c00921] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD+ and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have D2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism.
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Affiliation(s)
- Sai Rohit Guntupalli
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal University, Manipal, India.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Bryce V Plapp
- Department of Biochemistry, Bowen Science Building, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Ramaswamy Subramanian
- Department of Biological Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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Patel AY, Jonnalagadda KS, Paradis N, Vaden TD, Wu C, Caputo GA. Effects of Ionic Liquids on Metalloproteins. Molecules 2021; 26:514. [PMID: 33478102 PMCID: PMC7835893 DOI: 10.3390/molecules26020514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/28/2023] Open
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
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Affiliation(s)
- Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | | | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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