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Santema LL, Rozeboom HJ, Borger VP, Kaya SG, Fraaije MW. Identification of a robust bacterial pyranose oxidase which displays an unusual pH dependence. J Biol Chem 2024:107885. [PMID: 39395808 DOI: 10.1016/j.jbc.2024.107885] [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: 07/16/2024] [Revised: 09/30/2024] [Accepted: 10/06/2024] [Indexed: 10/14/2024] Open
Abstract
Pyranose oxidases are valuable biocatalysts, yet only a handful of bacterial pyranose oxidases are known. These bacterial enzymes exhibit noteworthy distinctions from their extensively characterized fungal counterparts, encompassing variations in substrate specificity and structural attributes. Herein a bacterial pyranose oxidase from Oscillatoria princeps (OPOx) was biochemically characterized in detail. In contrast to the fungal pyranose oxidases, OPOx could be well expressed in Escherichia coli as soluble, fully flavinylated and active oxidase. It was found to be highly thermostable (melting temperature >90 ⁰C) and showed activity on glucose, exhibiting an exceptionally low KM value (48 μM). Elucidation of its crystal structure revealed similarities with fungal pyranose oxidases, such as being a tetramer with a large central void leading to a narrow substrate access tunnel. In the active site, the FAD cofactor is covalently bound to a histidine. OPOx displays a relatively narrow pH optimum for activity with a sharp decline at relatively basic pH values which is accompanied with a drastic change in its flavin absorbance spectrum. The pH-dependent switch in flavin absorbance features and oxidase activity was shown to be fully reversible. It is hypothesized that a glutamic acid helps to stabilize the protonated form of the histidine that is tethered to the FAD. OPOx presents itself as a valuable biocatalyst as it is highly robust, well-expressed in E. coli, shows low KM values for monosaccharides and has a peculiar pH dependent "on-off switch".
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Affiliation(s)
- Lars L Santema
- Molecular Enzymology, University of Groningen, Nijenborgh 3, 9747AG Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Molecular Enzymology, University of Groningen, Nijenborgh 3, 9747AG Groningen, The Netherlands
| | - Veronica P Borger
- Molecular Enzymology, University of Groningen, Nijenborgh 3, 9747AG Groningen, The Netherlands
| | - Saniye G Kaya
- Molecular Enzymology, University of Groningen, Nijenborgh 3, 9747AG Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, Nijenborgh 3, 9747AG Groningen, The Netherlands.
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Kaushik S, Rameshwari R, Chapadgaonkar SS. The in-silico study of the structural changes in the Arthrobacter globiformis choline oxidase induced by high temperature. J Genet Eng Biotechnol 2024; 22:100348. [PMID: 38494262 PMCID: PMC10980864 DOI: 10.1016/j.jgeb.2023.100348] [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: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in 1933. However, the impact of the high temperature on its structure has not been explored despite the long history and availability of its crystal structure. Both choline oxidase and its product, glycine betaine, have enormous applications spanning across multiple industries. Understanding how the 3D structure of the enzyme will change with the temperature change can open new ways to make it more stable and useful for industry. PROCESS This research paper presents the in-silico study and analysis of the structural changes of A. globiformis choline oxidase at temperatures from 25 °C to 60 °C. A step-wise process is depicted in Fig. 1. RESULTS Multiple sequence alignment (MSA) of 11 choline oxidase sequences from different bacteria vs Arthrobacter globiformis choline oxidase showed that active site residues are highly conserved. The available crystal structure of A. globiformis choline oxidase with cofactor Flavin Adenine Dinucleotide (FAD) in the dimeric state (PDB ID: 4MJW)1 was considered for molecular dynamics simulations. A simulated annealing option was used to gradually increase the temperature of the system from 25 °C to 60 °C. Analysis of the conserved residues, as well as residues involved in Flavin Adenine Dinucleotide (FAD) binding, substrate binding, substate gating, and dimer formationwas done. At high temperatures, the formation of the inter-chain salt bridge between Arg50 and Glu63 was a significant observation near the active site of choline oxidase. CONCLUSION Molecular dynamics studies suggest that an increase in temperature has a significant impact on the extended Flavin Adenine Dinucleotide (FAD) binding region. These changes interfere with the entry of substrate to the active site of the enzyme and make the enzyme inactive.
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Affiliation(s)
- Sonia Kaushik
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Rashmi Rameshwari
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India.
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Lv Y, Chang J, Zhang W, Dong H, Chen S, Wang X, Zhao A, Zhang S, Alam MA, Wang S, Du C, Xu J, Wang W, Xu P. Improving Microbial Cell Factory Performance by Engineering SAM Availability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3846-3871. [PMID: 38372640 DOI: 10.1021/acs.jafc.3c09561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Methylated natural products are widely spread in nature. S-Adenosyl-l-methionine (SAM) is the secondary abundant cofactor and the primary methyl donor, which confer natural products with structural and functional diversification. The increasing demand for SAM-dependent natural products (SdNPs) has motivated the development of microbial cell factories (MCFs) for sustainable and efficient SdNP production. Insufficient and unsustainable SAM availability hinders the improvement of SdNP MCF performance. From the perspective of developing MCF, this review summarized recent understanding of de novo SAM biosynthesis and its regulatory mechanism. SAM is just the methyl mediator but not the original methyl source. Effective and sustainable methyl source supply is critical for efficient SdNP production. We compared and discussed the innate and relatively less explored alternative methyl sources and identified the one involving cheap one-carbon compound as more promising. The SAM biosynthesis is synergistically regulated on multilevels and is tightly connected with ATP and NAD(P)H pools. We also covered the recent advancement of metabolic engineering in improving intracellular SAM availability and SdNP production. Dynamic regulation is a promising strategy to achieve accurate and dynamic fine-tuning of intracellular SAM pool size. Finally, we discussed the design and engineering constraints underlying construction of SAM-responsive genetic circuits and envisioned their future applications in developing SdNP MCFs.
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Affiliation(s)
- Yongkun Lv
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Jinmian Chang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weiping Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Hanyu Dong
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Song Chen
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xian Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Anqi Zhao
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, China
| | - Shen Zhang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Md Asraful Alam
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Chaojun Du
- Nanyang Research Institute of Zhengzhou University, Nanyang Institute of Technology, No. 80 Changjiang Road, Nanyang 473004, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- National Key Laboratory of Biobased Transportation Fuel Technology, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Palo Alto, California 94305, United States
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China
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Immobilization of a Broad Range of Polypeptides on the Frustule of the Diatom Thalassiosira pseudonana. Appl Environ Microbiol 2022; 88:e0115322. [PMID: 36226967 PMCID: PMC9642022 DOI: 10.1128/aem.01153-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. One recently developed technique, living diatom silica immobilization (LiDSI), has made it possible to immobilize proteins, including multimeric and redox enzymes, via a cellular excretion system onto the silica frustule of the marine diatom Thalassiosira pseudonana. However, the number of application examples so far is limited, and the type of proteins appropriate for the technique is still enigmatic. Here, we applied LiDSI to six industrially relevant polypeptides, including protamine, metallothionein, phosphotriesterase, choline oxidase, laccase, and polyamine synthase. Protamine and metallothionein were successfully immobilized on the frustule as protein fusions with green fluorescent protein (GFP) at the N terminus, indicating that LiDSI can be used for polypeptides which are rich in arginine and cysteine. In contrast, we obtained mutants for the latter four enzymes in forms without green fluorescent protein. Immobilized phosphotriesterase, choline oxidase, and laccase showed enzyme activities even after the purification of frustule in the presence of 1% (wt/vol) octylphenoxy poly(ethyleneoxy)ethanol. An immobilized branched-chain polyamine synthase changed the intracellular polyamine composition and silica nanomorphology. These results illustrate the possibility of LiDSI for industrial applications. IMPORTANCE Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. Living diatom silica immobilization (LiDSI) is a recently developed technique for in vivo protein immobilization on the diatom frustule. We aimed to explore the possibility of using LiDSI for industrial applications by successfully immobilizing six polypeptides: (i) protamine (Oncorhynchus keta), a stable antibacterial agent; (ii) metallothionein (Saccharomyces cerevisiae), a metal adsorption molecule useful for bioremediation; (iii) phosphotriesterase (Sulfolobus solfataricus), a scavenger for toxic organic phosphates; (iv) choline oxidase (Arthrobacter globiformis), an enhancer for photosynthetic activity and yield of plants; (v) laccase (Bacillus subtilis), a phenol oxidase utilized for delignification of lignocellulosic materials; and (vi) branched-chain polyamine synthase (Thermococcus kodakarensis), which produces branched-chain polyamines important for DNA and RNA stabilization at high temperatures. This study provides new insights into the field of applied biological materials.
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Liu M, Liu H, Mei F, Yang N, Zhao D, Ai G, Xiang H, Zheng Y. Identification of the Biosynthetic Pathway of Glycine Betaine That Is Responsible for Salinity Tolerance in Halophilic Thioalkalivibrio versutus D301. Front Microbiol 2022; 13:875843. [PMID: 35516424 PMCID: PMC9062515 DOI: 10.3389/fmicb.2022.875843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/25/2022] [Indexed: 11/24/2022] Open
Abstract
Thioalkalivibrio versutus D301 has been widely used in the biodesulfurization process, as it is capable of oxidizing hydrogen sulfide to elemental sulfur under strongly halo-alkaline conditions. Glycine betaine contributes to the increased tolerance to extreme environments in some of Thioalkalivibrio species. However, the biosynthetic pathway of glycine betaine in Thioalkalivibrio remained unknown. Here, we found that genes associated with nitrogen metabolism of T. versutus D301 were significantly upregulated under high-salt conditions, causing the enhanced production of glycine betaine that functions as a main compatible solute in response to the salinity stress. Glycine betaine was synthesized by glycine methylation pathway in T. versutus D301, with glycine N-methyltransferase (GMT) and sarcosine dimethylglycine N-methyltransferase (SDMT) as key enzymes in this pathway. Moreover, substrate specificities of GMT and SDMT were quite different from the well characterized enzymes for glycine methylation in halophilic Halorhodospira halochloris. Our results illustrate the glycine betaine biosynthetic pathway in the genus of Thioalkalivibrio for the first time, providing us with a better understanding of the biosynthesis of glycine betaine in haloalkaliphilic Thioalkalivibrio.
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Affiliation(s)
- Mengshuang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hui Liu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Fangtong Mei
- College of Environment, Hohai University, Nanjing, China
| | - Niping Yang
- School of Life Sciences, Hebei University, Baoding, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yanning Zheng,
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Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence. Appl Microbiol Biotechnol 2022; 106:3153-3171. [PMID: 35396956 DOI: 10.1007/s00253-022-11906-1] [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: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 11/02/2022]
Abstract
The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB-up to 2.5 times, P450-up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. KEY POINTS: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome.
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Lokesha S, Ravi Kumar YS, Sujan Ganapathy PS, Gaur P, Arjun HM. Production of recombinant choline oxidase and its application in betaine production. 3 Biotech 2021; 11:410. [PMID: 34471592 DOI: 10.1007/s13205-021-02960-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/04/2021] [Indexed: 11/30/2022] Open
Abstract
Choline oxidase catalyzes the oxidation of choline to glycine betaine via betaine aldehyde in glycine betaine biosynthesis and betaine acts as an osmolyte. Choline oxidase has attracted a great deal of attention because of its wide application in clinical and its potential use in enzymatic betaine production. Therefore, the development of efficient methods for overexpression of choline oxidase will be very valuable. In the present study, the choline oxidase gene was amplified from a newly isolated Gram-positive soil Arthrobacter globiformis strain HYJE003 and was cloned into a pET expression vector. Furthermore, the culture conditions were optimized for overexpression of cloned choline oxidase gene in different hosts for periplasmic expression of the enzyme. Expression host system Rosetta-gami2(DE3)pLysS yielded more cell-free protein and 20 fold higher active enzyme compared to any other reported studies. Terrific Broth media were found to be yielding the highest cell biomass, by applying the optimized culture conditions and purification strategy 20,902 U of choline oxidase was produced with a specific activity of 95 U/mg. The optimum pH and temperature for the enzyme activity were found to be 7 and 37 °C, respectively. Finally, we have demonstrated efficient bioconversion of betaine using overexpressed and purified choline oxidase enzyme. The enzymatically produced betaine was estimated by the formation of betaine reineckate and we were able to produce 0.83 molar of betaine from one molar of choline chloride. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02960-z.
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Affiliation(s)
- S Lokesha
- Department of Biotechnology, M S Ramaiah Institute of Technology, MSR Nagar, Bangalore, Karnataka 560054 India
| | - Y S Ravi Kumar
- Department of Biotechnology, M S Ramaiah Institute of Technology, MSR Nagar, Bangalore, Karnataka 560054 India
| | - P S Sujan Ganapathy
- Nutrinorm Wellness Private Limited, No 508, 4th Floor, Medini, 60 Feet Road, Sahakarnagar, Bangalore, 560092 India
| | - Prashant Gaur
- Enzibeta Biotech Pvt. Ltd., IKP Knowledge Park, Genome Valley, Hyderabad, 500072 India
| | - H M Arjun
- Advanta Seeds Pvt. Ltd., Road No-7, Banjara Hills, Hyderabad, 500034 India
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Morpho-Physiological Testing of NaCl Sensitivity of Tobacco Plants Overexpressing Choline Oxidase Gene. PLANTS 2021; 10:plants10061102. [PMID: 34070894 PMCID: PMC8227115 DOI: 10.3390/plants10061102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
In this study the transgenic lines (TLs) of tobacco (Nicotianatabacum L.), which overexpress the heterologous gene encoding the bacterial enzyme choline oxidase were evaluated. The goal of our work is to study the effect of choline oxidase gene expression on the sensitivity of plant tissues to the action of NaCl. The regenerative capacity, rhizogenesis, the amount of photosynthetic pigments and osmotically active compounds (proline and glycine betaine) were assessed by in vitro cell culture methods using biochemical and morphological parameters. Transgenic lines with confirmed expression were characterized by high regeneration capacity from callus in the presence of 200 mmol NaCl, partial retention of viability at 400 mmol NaCl. These data correlated with the implicit response of regenerants and whole plants to the harmful effects of salinity. They turned out to be less sensitive to the presence of 200 mmol NaCl in the cultivation medium, in contrast to the WT plants.
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Kumar S, Paul D, Bhushan B, Wakchaure GC, Meena KK, Shouche Y. Traversing the "Omic" landscape of microbial halotolerance for key molecular processes and new insights. Crit Rev Microbiol 2020; 46:631-653. [PMID: 32991226 DOI: 10.1080/1040841x.2020.1819770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Post-2005, the biology of the salt afflicted habitats is predominantly studied employing high throughput "Omic" approaches comprising metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. Such "Omic-based" studies have deciphered the unfamiliar details about microbial salt-stress biology. The MAGs (Metagenome-assembled genomes) of uncultured halophilic microbial lineages such as Nanohaloarchaea and haloalkaliphilic members within CPR (Candidate Phyla Radiation) have been reconstructed from diverse hypersaline habitats. The study of MAGs of such uncultured halophilic microbial lineages has unveiled the genomic basis of salt stress tolerance in "yet to culture" microbial lineages. Furthermore, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. The present review focuses on the new insights into microbial salt-stress biology gained through different "Omic" approaches. This review also summarizes the key molecular processes that underlie microbial salt-stress response, and their role in microbial salt-stress tolerance has been confirmed at more than one "Omic" levels.
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Affiliation(s)
- Satish Kumar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.,ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, India
| | - Dhiraj Paul
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Bharat Bhushan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - G C Wakchaure
- ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, India
| | - Kamlesh K Meena
- ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
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Abstract
Choline oxidase catalyzes the four-electron, two-step, flavin-mediated oxidation of choline to glycine betaine. The enzyme is important both for medical and biotechnological reasons, because glycine betaine is one among a limited number of compatible solutes used by cells to counteract osmotic pressure. From a fundamental standpoint, choline oxidase has emerged as one of the paradigm enzymes for the oxidation of alcohols catalyzed by flavoproteins. Mechanistic, structural, and computational studies have elucidated the mechanism of action of the enzyme from Arthrobacter globiformis at the molecular level. Both choline and oxygen access to the active site cavity are gated and tightly controlled. Amino acid residues involved in substrate binding, and their contribution, have been identified. The mechanism of choline oxidation, with a hydride transfer reaction, an asynchronous transition state, the formation and stabilization of an alkoxide transient species, and a quantum mechanical mode of reaction, has been elucidated. The importance of nonpolar side chains for oxygen localization and of the positive charge harbored on the substrate for activation of oxygen for reaction with the reduced flavin have been recognized. Interesting phenomena, like the formation of a metastable photoinduced flavin-protein adduct, the reversible formation of a bicovalent flavoprotein, and the trapping of the enzyme in inactive conformations, have been described. This review summarizes the current status of our understanding on the structure-function-dynamics of choline oxidase.
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Affiliation(s)
- Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, United States; Department of Biology, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, United States.
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Das P, Behera BK, Chatterjee S, Das BK, Mohapatra T. De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes. PLoS One 2020; 15:e0228199. [PMID: 32040520 PMCID: PMC7010390 DOI: 10.1371/journal.pone.0228199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022] Open
Abstract
In the present study, we identified salt stress tolerant genes from the marine bacterium Staphylococcus sp. strain P-TSB-70 through transcriptome sequencing. In favour of whole-genome transcriptome profiling of Staphylococcus sp. strain P-TSB-70 (GenBank Accn. No. KP117091) which tolerated upto 20% NaCl stress, the strain was cultured in the laboratory condition with 20% NaCl stress. Transcriptome analyses were performed by SOLiD4.0 sequencing technology from which 10280 and 9612 transcripts for control and treated, respectively, were obtained. The coverage per base (CPB) statistics were analyzed for both the samples. Gene ontology (GO) analysis has been categorized at varied graph levels based on three primary ontology studies viz. cellular components, biological processes, and molecular functions. The KEGG analysis of the assembled transcripts using KAAS showed presumed components of metabolic pathways which perhaps implicated in diverse metabolic pathways responsible for salt tolerance viz. glycolysis/gluconeogenesis, oxidative phosphorylation, glutathione metabolism, etc. further involving in salt tolerance. Overall, 90 salt stress tolerant genes were identified as of 186 salt-related transcripts. Several genes have been found executing normally in the TCA cycle pathway, integral membrane proteins, generation of the osmoprotectants, enzymatic pathway associated with salt tolerance. Recognized genes fit diverse groups of salt stress genes viz. abc transporter, betaine, sodium antiporter, sodium symporter, trehalose, ectoine, and choline, that belong to different families of genes involved in the pathway of salt stress. The control sample of the bacterium showed elevated high proportion of transcript contigs (29%) while upto 20% salt stress treated sample of the bacterium showed a higher percentage of transcript contigs (31.28%). A total of 1,288 and 1,133 transcript contigs were measured entirely as novel transcript contigs in both control and treated samples, respectively. The structure and function of 10 significant salt stress tolerant genes of Staphylococcus sp. have been analyzed in this study. The information acquired in the present study possibly used to recognize and clone the salt stress tolerant genes and support in developing the salt stress-tolerant plant varieties to expand the agricultural productivity in the saline system.
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Affiliation(s)
- Priyanka Das
- Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Bijay Kumar Behera
- Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
- * E-mail:
| | - Soumendranath Chatterjee
- Parasitology and Microbiology Research Laboratory, Department of Zoology, University of Burdwan, Burdwan, West Bengal, India
| | - Basanta Kumar Das
- Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Trilochan Mohapatra
- Secretary, DARE and Director General, Indian Council of Agricultural Research, New Delhi, India
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Ronzheimer S, Warmbold B, Arnhold C, Bremer E. The GbsR Family of Transcriptional Regulators: Functional Characterization of the OpuAR Repressor. Front Microbiol 2018; 9:2536. [PMID: 30405586 PMCID: PMC6207618 DOI: 10.3389/fmicb.2018.02536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Accumulation of compatible solutes is a common stress response of microorganisms challenged by high osmolarity; it can be achieved either through synthesis or import. These processes have been intensively studied in Bacillus subtilis, where systems for the production of the compatible solutes proline and glycine betaine have been identified, and in which five transporters for osmostress protectants (Opu) have been characterized. Glycine betaine synthesis relies on the import of choline via the substrate-restricted OpuB system and the promiscuous OpuC transporter and its subsequent oxidation by the GbsAB enzymes. Transcription of the opuB and gbsAB operons is under control of the MarR-type regulator GbsR, which acts as an intracellular choline-responsive repressor. Modeling studies using the X-ray structure of the Mj223 protein from Methanocaldococcus jannaschii as the template suggest that GbsR is a homo-dimer with an N-terminal DNA-reading head and C-terminal dimerization domain; a flexible linker connects these two domains. In the vicinity of the linker region, an aromatic cage is predicted as the inducer-binding site, whose envisioned architecture resembles that present in choline and glycine betaine substrate-binding proteins of ABC transporters. We used bioinformatics to assess the phylogenomics of GbsR-type proteins and found that they are widely distributed among Bacteria and Archaea. Alignments of GbsR proteins and analysis of the genetic context of the corresponding structural genes allowed their assignment into four sub-groups. In one of these sub-groups of GbsR-type proteins, gbsR-type genes are associated either with OpuA-, OpuB-, or OpuC-type osmostress protectants uptake systems. We focus here on GbsR-type proteins, named OpuAR by us, that control the expression of opuA-type gene clusters. Using such a system from the marine bacterium Bacillus infantis, we show that OpuAR acts as a repressor of opuA transcription, where several compatible solutes (e.g., choline, glycine betaine, proline betaine) serve as its inducers. Site-directed mutagenesis studies allowed a rational improvement of the putative inducer-binding site in OpuAR with respect to the affinity of choline and glycine betaine binding. Collectively, our data characterize GbsR-/OpuAR-type proteins as an extended sub-group within the MarR-superfamily of transcriptional regulators and identify a novel type of substrate-inducible import system for osmostress protectants.
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Affiliation(s)
- Stefanie Ronzheimer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Bianca Warmbold
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Christian Arnhold
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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13
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Robbins JM, Bommarius AS, Gadda G. Mechanistic studies of formate oxidase from Aspergillus oryzae : A novel member of the glucose-Methanol-choline oxidoreductase enzyme superfamily that oxidizes carbon acids. Arch Biochem Biophys 2018; 643:24-31. [DOI: 10.1016/j.abb.2018.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/18/2018] [Accepted: 02/13/2018] [Indexed: 10/18/2022]
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14
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Wang KF, Liu CL, Sui KY, Guo C, Liu CZ. Efficient Catalytic Oxidation of 5-Hydroxymethylfurfural to 2,5-Furandicarboxylic Acid by Magnetic Laccase Catalyst. Chembiochem 2018; 19:654-659. [DOI: 10.1002/cbic.201800008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Ke-Feng Wang
- Institute of Biochemical Engineering; Collaborative Innovation Center for Marine Biomass Fibers; Materials and Textiles of Shandong Province; School of Materials Science and Engineering; Qingdao University; Qingdao 266071 China
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Chun-lei Liu
- Department of Urology; Qingdao Central Hospital; Qingdao 266042 China
| | - Kun-yan Sui
- Institute of Biochemical Engineering; Collaborative Innovation Center for Marine Biomass Fibers; Materials and Textiles of Shandong Province; School of Materials Science and Engineering; Qingdao University; Qingdao 266071 China
| | - Chen Guo
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 China
| | - Chun-Zhao Liu
- Institute of Biochemical Engineering; Collaborative Innovation Center for Marine Biomass Fibers; Materials and Textiles of Shandong Province; School of Materials Science and Engineering; Qingdao University; Qingdao 266071 China
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 China
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15
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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16
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Mass Spectrometry-Based Metabolomics of Agave Sap (Agave salmiana) after Its Inoculation with Microorganisms Isolated from Agave Sap Concentrate Selected to Enhance Anticancer Activity. SUSTAINABILITY 2017. [DOI: 10.3390/su9112095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1470-1478. [PMID: 28843728 DOI: 10.1016/j.bbapap.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/20/2022]
Abstract
The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[2H4]-choline as a substrate. The limiting rate constants klim1 and klim2 at saturating substrate were well separated (klim1/klim2>9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that klim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that klim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the klim1 and klim2 values increased with increasing temperature, allowing for the analyses of H+ and H- transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the klim1 value (H2Oklim1/D2Oklim1) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the klim2 value gave lines with the slope(choline)>slope(D-choline), suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed.
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18
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Salvi F, Rodriguez I, Hamelberg D, Gadda G. Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase. Biochemistry 2016; 55:1473-84. [PMID: 26907558 DOI: 10.1021/acs.biochem.5b01356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Choline oxidase from Arthrobacter globiformis catalyzes the oxidation of choline to glycine betaine by using oxygen as an electron acceptor. A partially rate limiting isomerization of the reduced wild-type enzyme during the reaction with oxygen was previously detected using solvent viscosity effects. In this study, we hypothesized that the side chains of M62 and F357, located at the entrance to the active site of choline oxidase, may be related to the slow isomerization detected. We engineered a double-variant enzyme M62A/F357A. The kinetic characterization of the double-variant enzyme showed a lack of the isomerization detected in wild-type choline oxidase, and a lack of saturation with an oxygen concentration as high as 1 mM, while most other kinetic parameters were similar to those of wild-type choline oxidase. The kinetic characterization of the single-variant enzymes established that only the side chain of F357 plays a role in the isomerization of choline oxidase in the oxidative half-reaction. Molecular dynamics studies suggest that the slow isomerization related to F357 is possibly due to the participation of the phenyl ring in a newly proposed gating mechanism for a narrow tunnel, assumed to regulate the access of oxygen to the reduced cofactor.
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Affiliation(s)
- Francesca Salvi
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Isela Rodriguez
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
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19
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Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, Wilkins JA, Cicek N, Sparling R, Levin DB. Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46. Appl Microbiol Biotechnol 2015; 99:5583-92. [PMID: 26002633 DOI: 10.1007/s00253-015-6685-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 01/29/2023]
Abstract
Biodiesel production-derived waste glycerol (WG) was previously investigated as potential carbon source for medium chain length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida LS46. In this study, we evaluated the effect of impurities in the WG on P. putida LS46 physiology during exponential growth and corresponding changes in transcription and protein expression profiles compared with cells grown on pure, reagent grade glycerol. High concentration of metal ions, such as Na(+), and numbers of heavy metals ion, such as copper, ion, zinc, were detected in biodiesel-derived WG. Omics analysis from the corresponding cultures suggested altered expression of genes involved in transport and metabolism of ammonia and heavy metal ions. Expression of three groups of heavy metal homeostasis genes was significantly changed (mostly upregulated) in WG cultures and included the following: copper-responded cluster 1 and 2 genes, primarily containing cusABC; two copies of copAB and heavy metal translocating P-type ATPase; Fur-regulated, TonB-dependent siderophore receptor; and several cobalt/zinc/cadmium transporters. Expression of these genes suggests regulation of intracellular concentrations of heavy metals during growth on biodiesel-derived glycerol. Finally, a number of genes involved in adapting to, or metabolizing free fatty acids and other nonheavy metal contaminants, such as Na(+), were also upregulated in P. putida LS46 grown on biodiesel-derived glycerol.
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Affiliation(s)
- Jilagamazhi Fu
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
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20
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Smitherman C, Rungsrisuriyachai K, Germann MW, Gadda G. Identification of the Catalytic Base for Alcohol Activation in Choline Oxidase. Biochemistry 2014; 54:413-21. [DOI: 10.1021/bi500982y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Crystal Smitherman
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Kunchala Rungsrisuriyachai
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Markus W. Germann
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
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21
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A multi-year assessment of the environmental impact of transgenic Eucalyptus trees harboring a bacterial choline oxidase gene on biomass, precinct vegetation and the microbial community. Transgenic Res 2014; 23:767-77. [PMID: 24927812 DOI: 10.1007/s11248-014-9809-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/30/2014] [Indexed: 12/24/2022]
Abstract
A 4-year field trial for the salt tolerant Eucalyptus globulus Labill. harboring the choline oxidase (codA) gene derived from the halobacterium Arthrobacter globiformis was conducted to assess the impact of transgenic versus non-transgenic trees on biomass production, the adjacent soil microbial communities and vegetation by monitoring growth parameters, seasonal changes in soil microbes and the allelopathic activity of leaves. Three independently-derived lines of transgenic E. globulus were compared with three independent non-transgenic lines including two elite clones. No significant differences in biomass production were detected between transgenic lines and non-transgenic controls derived from same seed bulk, while differences were seen compared to two elite clones. Significant differences in the number of soil microbes present were also detected at different sampling times but not between transgenic and non-transgenic lines. The allelopathic activity of leaves from both transgenic and non-transgenic lines also varied significantly with sampling time, but the allelopathic activity of leaves from transgenic lines did not differ significantly from those from non-transgenic lines. These results indicate that, for the observed variables, the impact on the environment of codA-transgenic E. globulus did not differ significantly from that of the non-transformed controls on this field trial.
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22
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Purification and Characterization of an Alkaliphilic Choline Oxidase ofFusarium oxysporum. Biosci Biotechnol Biochem 2014; 76:2219-24. [DOI: 10.1271/bbb.120513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Dijkman WP, Groothuis DE, Fraaije MW. Enzyme‐Catalyzed Oxidation of 5‐Hydroxymethylfurfural to Furan‐2,5‐dicarboxylic Acid. Angew Chem Int Ed Engl 2014; 53:6515-8. [DOI: 10.1002/anie.201402904] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Willem P. Dijkman
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen (The Netherlands) http://www.rug.nl/staff/m.w.fraaije/research
| | - Daphne E. Groothuis
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen (The Netherlands) http://www.rug.nl/staff/m.w.fraaije/research
| | - Marco W. Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen (The Netherlands) http://www.rug.nl/staff/m.w.fraaije/research
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24
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Dijkman WP, Groothuis DE, Fraaije MW. Enzyme‐Catalyzed Oxidation of 5‐Hydroxymethylfurfural to Furan‐2,5‐dicarboxylic Acid. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402904] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Willem P. Dijkman
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen (The Netherlands) http://www.rug.nl/staff/m.w.fraaije/research
| | - Daphne E. Groothuis
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen (The Netherlands) http://www.rug.nl/staff/m.w.fraaije/research
| | - Marco W. Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen (The Netherlands) http://www.rug.nl/staff/m.w.fraaije/research
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Biochemical analysis of recombinant AlkJ from Pseudomonas putida reveals a membrane-associated, flavin adenine dinucleotide-dependent dehydrogenase suitable for the biosynthetic production of aliphatic aldehydes. Appl Environ Microbiol 2014; 80:2468-77. [PMID: 24509930 DOI: 10.1128/aem.04297-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The noncanonical alcohol dehydrogenase AlkJ is encoded on the alkane-metabolizing alk operon of the mesophilic bacterium Pseudomonas putida GPo1. To gain insight into the enzymology of AlkJ, we have produced the recombinant protein in Escherichia coli and purified it to homogeneity using His6 tag affinity and size exclusion chromatography (SEC). Despite synthesis in the cytoplasm, AlkJ was associated with the bacterial cell membrane, and solubilization with n-dodecyl-β-D-maltoside was necessary to liberate the enzyme. SEC and spectrophotometric analysis revealed a dimeric quaternary structure with stoichiometrically bound reduced flavin adenine dinucleotide (FADH2). The holoenzyme showed thermal denaturation at moderate temperatures around 35°C, according to both activity assay and temperature-dependent circular dichroism spectroscopy. The tightly bound coenzyme was released only upon denaturation with SDS or treatment with urea-KBr and, after air oxidation, exhibited the characteristic absorption spectrum of FAD. The enzymatic activity of purified AlkJ for 1-butanol, 1-hexanol, and 1-octanol as well as the n-alkanol derivative ω-hydroxy lauric acid methyl ester (HLAMe) was quantified in the presence of the artificial electron acceptors phenazine methosulfate (PMS) and 2,6-dichlorophenolindophenol (DCPIP), indicating broad substrate specificity with the lowest activity on the shortest alcohol, 1-butanol. Furthermore, AlkJ was able to accept as cosubstrates/oxidants the ubiquinone derivatives Q0 and Q1, also in conjunction with cytochrome c, which suggests coupling to the bacterial respiratory chain of this membrane-associated enzyme in its physiological environment. Using gas chromatographic analysis, we demonstrated specific biocatalytic conversion by AlkJ of the substrate HLAMe to the industrially relevant aldehyde, thus enabling the biotechnological production of 12-amino lauric acid methyl ester via subsequent enzymatic transamination.
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Salvi F, Wang YF, Weber IT, Gadda G. Structure of choline oxidase in complex with the reaction product glycine betaine. ACTA ACUST UNITED AC 2014; 70:405-13. [DOI: 10.1107/s1399004713029283] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/23/2013] [Indexed: 11/10/2022]
Abstract
Choline oxidase fromArthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose–methanol–choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand–enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250–255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.
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Discovery and characterization of a 5-hydroxymethylfurfural oxidase from Methylovorus sp. strain MP688. Appl Environ Microbiol 2013; 80:1082-90. [PMID: 24271187 DOI: 10.1128/aem.03740-13] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein from Methylovorus sp. strain MP688 in Escherichia coli and subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations.
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28
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Salvi F, Gadda G. Human choline dehydrogenase: medical promises and biochemical challenges. Arch Biochem Biophys 2013; 537:243-52. [PMID: 23906661 PMCID: PMC7094428 DOI: 10.1016/j.abb.2013.07.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/24/2013] [Accepted: 07/16/2013] [Indexed: 01/17/2023]
Abstract
Human choline dehydrogenase (CHD) is located in the inner membrane of mitochondria primarily in liver and kidney and catalyzes the oxidation of choline to glycine betaine. Its physiological role is to regulate the concentrations of choline and glycine betaine in the blood and cells. Choline is important for regulation of gene expression, the biosynthesis of lipoproteins and membrane phospholipids and for the biosynthesis of the neurotransmitter acetylcholine; glycine betaine plays important roles as a primary intracellular osmoprotectant and as methyl donor for the biosynthesis of methionine from homocysteine, a required step for the synthesis of the ubiquitous methyl donor S-adenosyl methionine. Recently, CHD has generated considerable medical attention due to its association with various human pathologies, including male infertility, homocysteinuria, breast cancer and metabolic syndrome. Despite the renewed interest, the biochemical characterization of the enzyme has lagged behind due to difficulties in the obtainment of purified, active and stable enzyme. This review article summarizes the medical relevance and the physiological roles of human CHD, highlights the biochemical knowledge on the enzyme, and provides an analysis based on the comparison of the protein sequence with that of bacterial choline oxidase, for which structural and biochemical information is available.
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Affiliation(s)
- Francesca Salvi
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-3965, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-3965, United States
- Department of Biology, Georgia State University, Atlanta, GA 30302-3965, United States
- The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-3965, United States
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Rubiano-Labrador C, Bland C, Miotello G, Guérin P, Pible O, Baena S, Armengaud J. Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring. J Proteomics 2013; 97:36-47. [PMID: 23727365 DOI: 10.1016/j.jprot.2013.05.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 04/30/2013] [Accepted: 05/16/2013] [Indexed: 01/18/2023]
Abstract
UNLABELLED Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions. At low salinity general stress proteins (chaperons, proteases and proteins associated with oxidative stress protection), were detected in higher amounts, probably linked to difficulties for proper protein folding and metabolism. Proteogenomics and comparative genomics pointed at the CrgA transcriptional regulator as a key-factor for the proteome remodeling upon low osmolarity. In hyper-osmotic condition, T. consotensis produced in larger amounts proteins involved in the sensing of changes in salt concentration, as well as a wide panel of transport systems for the transport of organic compatible solutes such as glutamate. We have described here a straightforward procedure in making a new environmental isolate quickly amenable to proteomics. BIOLOGICAL SIGNIFICANCE The bacterium Tistlia consotensis was isolated from a saline spring in the Colombian Andes and represents an interesting environmental model to be compared with extremophiles or other moderate organisms. To explore the halotolerance molecular mechanisms of the bacterium T. consotensis, we developed an innovative proteogenomic strategy consisting of i) genome sequencing, ii) quick annotation of the genes whose products were detected by mass spectrometry, and iii) comparative proteomics of cells grown in three salt conditions. We highlighted in this manuscript how efficient such an approach can be compared to time-consuming genome annotation when pointing at the key proteins of a given biological question. We documented a large number of proteins found produced in greater amounts when cells are cultivated in either hypo-osmotic or hyper-osmotic conditions. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Carolina Rubiano-Labrador
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá D.C., Colombia; Colombian Center for Genomics and Bioinformatics of Extreme Environments, GeBiX, Colombia
| | - Céline Bland
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Guylaine Miotello
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Philippe Guérin
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá D.C., Colombia; Colombian Center for Genomics and Bioinformatics of Extreme Environments, GeBiX, Colombia
| | - Jean Armengaud
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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Flavoprotein oxidases: classification and applications. Appl Microbiol Biotechnol 2013; 97:5177-88. [PMID: 23640366 DOI: 10.1007/s00253-013-4925-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
This review provides an overview of oxidases that utilise a flavin cofactor for catalysis. This class of oxidative flavoenzymes has shown to harbour a large number of biotechnologically interesting enzymes. Applications range from their use as biocatalysts for the synthesis of pharmaceutical compounds to the integration in biosensors. Through the recent developments in genome sequencing, the number of newly discovered oxidases is steadily growing. Recent progress in the field of flavoprotein oxidase discovery and the obtained biochemical knowledge on these enzymes are reviewed. Except for a structure-based classification of known flavoprotein oxidases, also their potential in recent biotechnological applications is discussed.
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Pathway of glycine betaine biosynthesis in Aspergillus fumigatus. EUKARYOTIC CELL 2013; 12:853-63. [PMID: 23563483 DOI: 10.1128/ec.00348-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The choline oxidase (CHOA) and betaine aldehyde dehydrogenase (BADH) genes identified in Aspergillus fumigatus are present as a cluster specific for fungal genomes. Biochemical and molecular analyses of this cluster showed that it has very specific biochemical and functional features that make it unique and different from its plant and bacterial homologs. A. fumigatus ChoAp catalyzed the oxidation of choline to glycine betaine with betaine aldehyde as an intermediate and reduced molecular oxygen to hydrogen peroxide using FAD as a cofactor. A. fumigatus Badhp oxidized betaine aldehyde to glycine betaine with reduction of NAD(+) to NADH. Analysis of the AfchoAΔ::HPH and AfbadAΔ::HPH single mutants and the AfchoAΔAfbadAΔ::HPH double mutant showed that AfChoAp is essential for the use of choline as the sole nitrogen, carbon, or carbon and nitrogen source during the germination process. AfChoAp and AfBadAp were localized in the cytosol of germinating conidia and mycelia but were absent from resting conidia. Characterization of the mutant phenotypes showed that glycine betaine in A. fumigatus functions exclusively as a metabolic intermediate in the catabolism of choline and not as a stress protectant. This study in A. fumigatus is the first molecular, cellular, and biochemical characterization of the glycine betaine biosynthetic pathway in the fungal kingdom.
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Gannavaram S, Gadda G. Relative Timing of Hydrogen and Proton Transfers in the Reaction of Flavin Oxidation Catalyzed by Choline Oxidase. Biochemistry 2013; 52:1221-6. [DOI: 10.1021/bi3016235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Swathi Gannavaram
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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Yuan H, Gadda G. Importance of a Serine Proximal to the C(4a) and N(5) Flavin Atoms for Hydride Transfer in Choline Oxidase. Biochemistry 2011; 50:770-9. [DOI: 10.1021/bi101837u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Giovanni Gadda
- Department of Chemistry
- Department of Biology
- The Center for Biotechnology and Drug Design
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34
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Monnet C, Loux V, Gibrat JF, Spinnler E, Barbe V, Vacherie B, Gavory F, Gourbeyre E, Siguier P, Chandler M, Elleuch R, Irlinger F, Vallaeys T. The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PLoS One 2010; 5:e15489. [PMID: 21124797 PMCID: PMC2991359 DOI: 10.1371/journal.pone.0015489] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 09/24/2010] [Indexed: 11/18/2022] Open
Abstract
Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+)/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.
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Affiliation(s)
- Christophe Monnet
- INRA, UMR782 Génie et microbiologie des procédés alimentaires, Thiverval-Grignon, France.
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35
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Maeda Y, Doubayashi D, Ootake T, Oki M, Mikami B, Uchida H. Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1064-6. [PMID: 20823527 DOI: 10.1107/s1744309110028605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/17/2010] [Indexed: 05/26/2023]
Abstract
Formate oxidase (FOD), which catalyzes the oxidation of formate to yield carbon dioxide and hydrogen peroxide, belongs to the glucose-methanol-choline oxidoreductase (GMCO) family. FOD from Aspergillus oryzae RIB40, which has a modified FAD as a cofactor, was crystallized at 293 K by the hanging-drop vapour-diffusion method. The crystal was orthorhombic and belonged to space group C222(1). Diffraction data were collected from a single crystal to 2.4 A resolution.
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Affiliation(s)
- Yoshifumi Maeda
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 9-1 Bunkyo 3-chome, Fukui-shi 910-8507, Japan
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36
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Finnegan S, Yuan H, Wang YF, Orville AM, Weber IT, Gadda G. Structural and kinetic studies on the Ser101Ala variant of choline oxidase: catalysis by compromise. Arch Biochem Biophys 2010; 501:207-13. [PMID: 20561507 DOI: 10.1016/j.abb.2010.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 06/10/2010] [Accepted: 06/10/2010] [Indexed: 11/27/2022]
Abstract
The oxidation of choline catalyzed by choline oxidase includes two reductive half-reactions where FAD is reduced by the alcohol substrate and by an aldehyde intermediate transiently formed in the reaction. Each reductive half-reaction is followed by an oxidative half-reaction where the reduced flavin is oxidized by oxygen. Here, we have used mutagenesis to prepare the Ser101Ala mutant of choline oxidase and have investigated the impact of this mutation on the structural and kinetic properties of the enzyme. The crystallographic structure of the Ser101Ala enzyme indicates that the only differences between the mutant and wild-type enzymes are the lack of a hydroxyl group on residue 101 and a more planar configuration of the flavin in the mutant enzyme. Kinetics established that replacement of Ser101 with alanine yields a mutant enzyme with increased efficiencies in the oxidative half-reactions and decreased efficiencies in the reductive half-reactions. This is accompanied by a significant decrease in the overall rate of turnover with choline. Thus, this mutation has revealed the importance of a specific residue for the optimization of the overall turnover of choline oxidase, which requires fine-tuning of four consecutive half-reactions for the conversion of an alcohol to a carboxylic acid.
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Affiliation(s)
- Steffan Finnegan
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, USA
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37
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Finnegan S, Agniswamy J, Weber IT, Gadda G. Role of Valine 464 in the Flavin Oxidation Reaction Catalyzed by Choline Oxidase,. Biochemistry 2010; 49:2952-61. [DOI: 10.1021/bi902048c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Irene T. Weber
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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38
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Rungsrisuriyachai K, Gadda G. Role of Asparagine 510 in the Relative Timing of Substrate Bond Cleavages in the Reaction Catalyzed by Choline Oxidase. Biochemistry 2010; 49:2483-90. [DOI: 10.1021/bi901796a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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39
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Quaye O, Cowins S, Gadda G. Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase. J Biol Chem 2009; 284:16990-16997. [PMID: 19398559 DOI: 10.1074/jbc.m109.003715] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FAD-dependent choline oxidase has a flavin cofactor covalently attached to the protein via histidine 99 through an 8alpha-N(3)-histidyl linkage. The enzyme catalyzes the four-electron oxidation of choline to glycine betaine, forming betaine aldehyde as an enzyme-bound intermediate. The variant form of choline oxidase in which the histidine residue has been replaced with asparagine was used to investigate the contribution of the 8alpha-N(3)-histidyl linkage of FAD to the protein toward the reaction catalyzed by the enzyme. Decreases of 10-fold and 30-fold in the k(cat)/K(m) and k(cat) values were observed as compared with wild-type choline oxidase at pH 10 and 25 degrees C, with no significant effect on k(cat)/K(O) using choline as substrate. Both the k(cat)/K(m) and k(cat) values increased with increasing pH to limiting values at high pH consistent with the participation of an unprotonated group in the reductive half-reaction and the overall turnover of the enzyme. The pH independence of both (D)(k(cat)/K(m)) and (D)k(cat), with average values of 9.2 +/- 3.3 and 7.4 +/- 0.5, respectively, is consistent with absence of external forward and reverse commitments to catalysis, and the chemical step of CH bond cleavage being rate-limiting for both the reductive half-reaction and the overall enzyme turnover. The temperature dependence of the (D)k(red) values suggests disruption of the preorganization in the asparagine variant enzyme. Altogether, the data presented in this study are consistent with the FAD-histidyl covalent linkage being important for the optimal positioning of the hydride ion donor and acceptor in the tunneling reaction catalyzed by choline oxidase.
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Affiliation(s)
- Osbourne Quaye
- From the Departments of Chemistry, Atlanta, Georgia 30302-4098
| | - Sharonda Cowins
- From the Departments of Chemistry, Atlanta, Georgia 30302-4098; Department of Chemistry, Albany State University, Albany, Georgia 31705
| | - Giovanni Gadda
- From the Departments of Chemistry, Atlanta, Georgia 30302-4098; Biology, Atlanta, Georgia 30302-4098; The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098.
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40
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Orville AM, Lountos GT, Finnegan S, Gadda G, Prabhakar R. Crystallographic, spectroscopic, and computational analysis of a flavin C4a-oxygen adduct in choline oxidase. Biochemistry 2009; 48:720-8. [PMID: 19133805 DOI: 10.1021/bi801918u] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavin C4a-OO(H) and C4a-OH adducts are critical intermediates proposed in many flavoenzyme reaction mechanisms, but they are rarely detected even by rapid transient kinetics methods. We observe a trapped flavin C4a-OH or C4a-OO(H) adduct by single-crystal spectroscopic methods and in the 1.86 A resolution X-ray crystal structure of choline oxidase. The microspectrophotometry results show that the adduct forms rapidly in situ at 100 K upon exposure to X-rays. Density functional theory calculations establish the electronic structures for the flavin C4a-OH and C4a-OO(H) adducts and estimate the stabilization energy of several active site hydrogen bonds deduced from the crystal structure. We propose that the enzyme-bound FAD is reduced in the X-ray beam. The aerobic crystals then form either a C4a-OH or C4a-OO(H) adduct, but an insufficient proton inventory prevents their decay at cryogenic temperatures.
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Affiliation(s)
- Allen M Orville
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973-5000, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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41
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Gadda G. Hydride transfer made easy in the reaction of alcohol oxidation catalyzed by flavin-dependent oxidases. Biochemistry 2009; 47:13745-53. [PMID: 19053234 DOI: 10.1021/bi801994c] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Choline oxidase (E.C. 1.1.3.17; choline-oxygen 1-oxidoreductase) catalyzes the two-step, four-electron oxidation of choline to glycine betaine with betaine aldehyde as enzyme-associated intermediate and molecular oxygen as final electron acceptor. Biochemical, structural, and mechanistic studies on the wild-type and a number of mutant forms of choline oxidase from Arthrobacter globiformis have recently been carried out, allowing for the delineation at molecular and atomic levels of the mechanism of alcohol oxidation catalyzed by the enzyme. First, the alcohol substrate is activated to its alkoxide species by the removal of the hydroxyl proton in the enzyme-substrate complex. The resulting activated alkoxide is correctly positioned for catalysis through electrostatic and hydrogen bonding interactions with a number of active site residues. After substrate activation and correct positioning are attained, alcohol oxidation occurs in a highly preorganized enzyme-substrate complex through quantum mechanical transfer of a hydride ion from the alpha-carbon of the chelated, alkoxide species to the N(5) atom of the enzyme-bound flavin. This mechanism in its essence is shared by another class of alcohol oxidizing enzymes that utilize a catalytic zinc to stabilize an alkoxide intermediate and NAD(P)(+) as the organic cofactor that accepts the hydride ion, whose paradigm example is alcohol dehydrogenase. It will be interesting to experimentally evaluate the attractive hypothesis of whether the mechanism of choline oxidase can be extended to other flavin-dependent enzymes as well as enzymes that utilize cofactors other than flavins in the oxidation of alcohols.
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Affiliation(s)
- Giovanni Gadda
- Departments of Chemistry and Biology, and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA.
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42
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Finnegan S, Gadda G. Substitution of an active site valine uncovers a kinetically slow equilibrium between competent and incompetent forms of choline oxidase. Biochemistry 2009; 47:13850-61. [PMID: 19053262 DOI: 10.1021/bi801424p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic oxidation of choline to glycine betaine is of interest because organisms accumulate glycine betaine intracellularly in response to stress conditions. This is relevant for the genetic engineering of crops with economic interest that do not naturally possess efficient pathways for the synthesis of glycine betaine and for the potential development of drugs that target the glycine betaine biosynthetic pathway in human pathogens. To date, the best characterized choline-oxidizing enzyme is the flavin-dependent choline oxidase from Arthrobacter globiformis, for which structural, mechanistic, and biochemical data are available. Here, we have replaced a hydrophobic residue (Val464) lining the active site cavity close to the N(5) atom of the flavin with threonine or alanine to investigate its role in the reaction of choline oxidation catalyzed by choline oxidase. The reductive half-reactions of the enzyme variants containing Thr464 or Ala464 were investigated using substrate and solvent kinetic isotope effects, solvent viscosity effects, and proton inventories. Replacement of Val464 with threonine or alanine uncovered a kinetically slow equilibrium between a catalytically incompetent form of enzyme and an active species that can efficiently oxidize choline. In both variants, the active form of enzyme shows a decreased rate of hydroxyl proton abstraction from the alcohol substrate, with minimal changes in the subsequent rate of hydride ion transfer to the flavin. This study therefore establishes that a hydrophobic residue not directly participating in catalysis plays important roles in the reaction of choline oxidation catalyzed by choline oxidase.
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Affiliation(s)
- Steffan Finnegan
- Departments of Chemistry and Biology, The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA
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43
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Heterologous expression and characterization of Choline Oxidase from the soil bacterium Arthrobacter nicotianae. Appl Microbiol Biotechnol 2009; 81:875-86. [DOI: 10.1007/s00253-008-1661-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 07/30/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
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44
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Recovery of choline oxidase activity by in vitro recombination of individual segments. Appl Microbiol Biotechnol 2008; 81:275-82. [DOI: 10.1007/s00253-008-1605-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 06/25/2008] [Accepted: 07/03/2008] [Indexed: 11/29/2022]
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45
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Gu ZJ, Wang L, Le Rudulier D, Zhang B, Yang SS. Characterization of the Glycine Betaine Biosynthetic Genes in the Moderately Halophilic Bacterium Halobacillus dabanensis D-8T. Curr Microbiol 2008; 57:306-11. [DOI: 10.1007/s00284-008-9194-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 04/25/2008] [Indexed: 10/21/2022]
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46
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Rungsrisuriyachai K, Gadda G. On the Role of Histidine 351 in the Reaction of Alcohol Oxidation Catalyzed by Choline Oxidase. Biochemistry 2008; 47:6762-9. [DOI: 10.1021/bi800650w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kunchala Rungsrisuriyachai
- Departments of Chemistry and Biology and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098
| | - Giovanni Gadda
- Departments of Chemistry and Biology and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098
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Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2007; 2:e214. [PMID: 17194220 PMCID: PMC1713258 DOI: 10.1371/journal.pgen.0020214] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 11/02/2006] [Indexed: 01/24/2023] Open
Abstract
Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals. Soil systems contain the greatest diversity of microorganisms on earth, with 5,000–10,000 species of microorganism per gram of soil. Arthrobacter sp. strains have a primitive life cycle and are among the most frequently isolated, indigenous soil bacteria, found in common and deep subsurface soils, arctic ice, and environments contaminated with industrial chemicals and radioactive materials. To better understand how these bacteria survive in environmentally harsh conditions, the authors used a structural genomics approach to identify genes involved in soil survival of Arthrobacter aurescens strain TC1, a bacterium originally isolated for its ability to degrade the herbicide atrazine. They found that the genome of this bacterium comprises a single circular chromosome and two plasmids that encode for a large number proteins involved in stress responses due to starvation, desiccation, oxygen radicals, and toxic chemicals. A. aurescens' metabolic versatility is in part due to the presence of duplicated catabolic genes and its ability to funnel plasmid-derived intermediates into chromosomally encoded pathways. Arthrobacter's array of genes that allow for survival in stressful conditions and its ability to produce a temperature-tolerant “cyst”-like resting cell render this soil microorganism able to survive and prosper in a variety of environmental conditions.
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Affiliation(s)
- Emmanuel F Mongodin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Nir Shapir
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Sean C Daugherty
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Joanne B Emerson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Alla Shvartzbeyn
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Diana Radune
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Jessica Vamathevan
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Florenta Riggs
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Viktoria Grinberg
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Lawrence P Wackett
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Karen E Nelson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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48
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Mitchell J, Siboo IR, Takamatsu D, Chambers HF, Sullam PM. Mechanism of cell surface expression of the Streptococcus mitis platelet binding proteins PblA and PblB. Mol Microbiol 2007; 64:844-57. [PMID: 17462028 DOI: 10.1111/j.1365-2958.2007.05703.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PblA and PblB are prophage-encoded proteins of Streptococcus mitis strain SF100 that mediate binding to human platelets. The mechanism for surface expression of these proteins has been unknown, as they do not contain signal sequences or cell wall sorting motifs. We therefore assessed whether expression of these proteins was linked the lytic cycle of the prophage. Deletion of either the holin or lysin gene resulted in retention of PblA and PblB in the cytoplasm, and loss of these proteins from the cell wall. Flow cytometric analysis revealed that induction of phage replication in SF100 produced a subpopulation of cells with increased permeability. This effect was abrogated by disruption of the holin and lysin genes. Treatment of these mutants with exogenous PblA and PblB restored surface expression, apparently via binding of the proteins to cell wall choline. Loss of PblA and PblB expression was associated with decreased platelet binding in vitro, and reduced virulence in an animal model of endocarditis. Thus, expression of PblA and PblB occurs via a novel mechanism, whereby phage induction increases bacterial permeability and release of the proteins, followed by their binding to surface of viable cells. This mechanism may be important for endovascular infection.
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Affiliation(s)
- Jennifer Mitchell
- Veterans Affairs Medical Center and the University of California, San Francisco, CA 94121, USA
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49
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Abstract
Choline oxidase catalyzes the oxidation of choline to glycine-betaine, with betaine-aldehyde as intermediate and molecular oxygen as primary electron acceptor. This study reports on the inhibitory effects of triarylmethanes (cationic malachite green; neutral leukomalachite green), phenoxazines (cationic, meldola blue and nile blue; neutral nile red) and a structurally-related phenothiazine (methylene blue) on choline oxidase, assayed at 25 degrees C in 50 mM MOPS buffer, pH 7, using choline as substrate. Methylene B acted as a competitive inhibitor with K(i) = 74 +/- 7.2 microM, pointing to the choline-binding site of the enzyme as a target site. Nile B caused noncompetitive inhibition of enzyme activity with K(i) = 20 +/- 4.5 microM. In contrast to methylene B and nile B, malachite G and meldola B caused complex, nonlinear inhibition of choline oxidase, with estimated K(i) values in the micromolar range. The difference in kinetic pattern was ascribed to the differential ability of the dyes to interact (and interfere) with the flavin cofactor, generating different perturbations in the steady-state balance of the catalytic process.
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Affiliation(s)
- Ozden Tacal
- Department of Biochemistry, School of Pharmacy, Hacettepe University, 06100 Ankara, Turkey.
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50
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Hoang JV, Gadda G. Trapping choline oxidase in a nonfunctional conformation by freezing at low pH. Proteins 2006; 66:611-20. [PMID: 17143885 DOI: 10.1002/prot.21238] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Choline oxidase is a flavin-dependent enzyme that catalyzes the oxidation of choline to glycine-betaine, with oxygen as electron acceptor. Storage at pH 6 and -20 degrees C resulted in a change in the conformation of choline oxidase, which was associated with complete loss of catalytic activity when the enzyme was assayed at pH 6. Incubation of the inactive enzyme at pH values > or = 6.5 and 25 degrees C resulted in a fast and partial reactivation of the enzyme, which occurred with slow onset of steady state during enzymatic turnover. The rate of approaching steady state was independent of the concentrations of choline and enzyme, but increased to a limiting value with increasing pH, defining a pKa value of approximately 7.3 for an unprotonated group required for enzyme activation. Prolonged incubation of the inactive enzyme at pH 6 and temperatures > or = 20 degrees C, at which no hysteretic behavior was observed, resulted in the slow and full recovery of activity over 3 h, associated with a conformational change that reverted the enzyme to the native form. Activation of the enzyme at pH 6 was enthalpy-driven with deltaH(double dagger) and TdeltaS(double dagger) values of approximately 112 kJ mol(-1) and approximately 20 kJ mol(-1) determined at 25 degrees C. These data suggest that freezing the enzyme at low pH induces a localized and reversible conformational change that is associated with the complete and reversible loss of catalytic activity.
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Affiliation(s)
- Jane V Hoang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, USA
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