1
|
Forero N, Liu C, Sabbah SG, Loewen MC, Yang TC. Assay Development for Metal-Dependent Enzymes-Influence of Reaction Buffers on Activities and Kinetic Characteristics. ACS OMEGA 2023; 8:40119-40127. [PMID: 37929113 PMCID: PMC10620931 DOI: 10.1021/acsomega.3c02835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023]
Abstract
Buffers are often thought of as innocuous components of a reaction, with the sole task of maintaining the pH of a system. However, studies had shown that this is not always the case. Common buffers used in biochemical research, such as Tris (hydroxymethyl) aminomethane hydrochloride (Tris-HCl), can chelate metal ions and may thus affect the activity of metalloenzymes, which are enzymes that require metal ions for enhanced catalysis. To determine whether enzyme activity is influenced by buffer identity, the activity of three enzymes (BLC23O, Ro1,2-CTD, and trypsin) was comparatively characterized in N-2- hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES), Tris-HCl, and sodium phosphate buffer. The pH and temperature optima of BLC23O, a Mn2+-dependent dioxygenase, were first identified, and then the metal ion dissociation constant (Kd) was determined in the three buffer systems. It was observed that BLC23O exhibited different Kd values depending on the buffer, with the lowest (1.49 ± 0.05 μM) recorded in HEPES under the optimal set of conditions (pH 7.6 and 32.5 °C). Likewise, the kinetic parameters obtained varied depending on the buffer, with HEPES (pH 7.6) yielding overall the greatest catalytic efficiency and turnover number (kcat = 0.45 ± 0.01 s-1; kcat/Km = 0.84 ± 0.02 mM-1 s-1). To corroborate findings, the characterization of Fe3+-dependent Ro1,2-CTD was performed, resulting in different kinetic constants depending on the buffer (Km (HEPES, Tris-HCl, and Na-phosphate) = 1.80, 6.93, and 3.64 μM; kcat(HEPES, Tris-HCl, and Na-phosphate) = 0.64, 1.14, and 1.01 s-1; kcat/Km(HEPES, Tris-HCl, and Na-phosphate)= 0.36, 0.17, and 0.28 μM-1 s-1). In order to determine whether buffer identity influenced the enzymatic activity of nonmetalloenzymes alike, the characterization of trypsin was also carried out. Contrary to the previous results, trypsin yielded comparable kinetic parameters independent of the buffer (Km (HEPES, Tris-HCl, and Na-Phosphate) = 3.14, 3.07, and 2.91 mM; kcat(HEPES, Tris-HCl, and Na-phosphate) = 1.51, 1.47, and 1.53 s-1; kcat/Km (HEPES, Tris-HCl, and Na-phosphate) = 0.48, 0.48, and 0.52 mM-1 s-1). These results showed that the activity of tested metalloenzymes was impacted by different buffers. While selected buffers did not influence the tested nonmetalloenzyme activity, other research had shown impacts of buffers on other enzyme activities. As a result, we suggest that buffer selection be optimized for any new enzymes such that the results from one lab to another can be accurately compared.
Collapse
Affiliation(s)
- Natalia Forero
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Chengsong Liu
- Aquatic
and Crop Resource Development Research Centre, National Research Council, Ottawa K1A 0R6, Canada
| | | | - Michele C. Loewen
- Aquatic
and Crop Resource Development Research Centre, National Research Council, Ottawa K1A 0R6, Canada
| | - Trent Chunzhong Yang
- Aquatic
and Crop Resource Development Research Centre, National Research Council, Ottawa K1A 0R6, Canada
| |
Collapse
|
2
|
Liu N, Li D, Li K, Wang L, Xu R, Zhang J, Yang B. Enhanced biodegradation of chlorobenzene via combined Fe 3+ and Zn 2+ based on rhamnolipid solubilisation. J Environ Sci (China) 2021; 103:108-118. [PMID: 33743893 DOI: 10.1016/j.jes.2020.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Biotrickling filters (BTFs) for hydrophobic chlorobenzene (CB) purification are limited by mass transfer and biodegradation. The CB mass transfer rate could be improved by 150 mg/L rhamnolipids. This study evaluated the combined use of Fe3+ and Zn2+ to enhance biodegradation in a BTF over 35 day. The effects of these trace elements were analysed under different inlet concentrations (250, 600, 900, and 1200 mg/L) and empty bed residence times (EBRTs; 60, 45, and 32 sec). Batch experiments showed that the promoting effects of Fe3+/Zn2+ on microbial growth and metabolism were highest for 3 mg/L Fe3+ and 2 mg/L Zn2+, followed by 2 mg/L Zn2+, and lowest at 3 mg/L Fe3+. Compared to BTF in the absence of Fe3+ and Zn2+, the average CB elimination capacity and removal efficiency in the presence of Fe3+ and Zn2+ increased from 61.54 to 65.79 g/(m3⋅hr) and from 80.93% to 89.37%, respectively, at an EBRT of 60 sec. The average removal efficiency at EBRTs of 60, 45, and 32 sec increased by 2.89%, 5.63%, and 11.61%, respectively. The chemical composition (proteins (PN), polysaccharides (PS)) and functional groups of the biofilm were analysed at 60, 81, and 95 day. Fe3+ and Zn2+ significantly enhanced PN and PS secretion, which may have promoted CB adsorption and biodegradation. High-throughput sequencing revealed the promoting effect of Fe3+ and Zn2+ on bacterial populations. The combination of Fe3+ and Zn2+ with rhamnolipids was an efficient method for improving CB biodegradation in BTFs.
Collapse
Affiliation(s)
- Na Liu
- Engineering Research Center of Mine Ecological Construction, Ministry of Education, China University of Mining and Technology, Xuzhou 221116, China
| | - Dan Li
- Engineering Research Center of Mine Ecological Construction, Ministry of Education, China University of Mining and Technology, Xuzhou 221116, China
| | - Kang Li
- Engineering Research Center of Mine Ecological Construction, Ministry of Education, China University of Mining and Technology, Xuzhou 221116, China
| | - Liping Wang
- Engineering Research Center of Mine Ecological Construction, Ministry of Education, China University of Mining and Technology, Xuzhou 221116, China.
| | - Ruiwei Xu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jiaming Zhang
- Engineering Research Center of Mine Ecological Construction, Ministry of Education, China University of Mining and Technology, Xuzhou 221116, China
| | - Bairen Yang
- School of Environmental Science and Engineering, Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Yancheng 224051, China
| |
Collapse
|
3
|
Johnson WH, Stack TMM, Taylor SM, Burks EA, Whitman CP. Stereochemical Consequences of Vinylpyruvate Hydratase-Catalyzed Reactions. Biochemistry 2016; 55:4055-64. [PMID: 27362840 DOI: 10.1021/acs.biochem.6b00552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A stereochemical analysis has been carried out on two vinylpyruvate hydratases (VPH), which convert 2-hydroxy-2,4-pentadienoate to 2-keto-4S-hydroxypentanoate in meta-fission pathways. Bacterial strains with this pathway can use aromatic compounds as sole sources of energy and carbon. The analysis was carried out using the 5-methyl and 5-chloro derivatives of 2-hydroxy-2,4-pentadienoate with the enzymes from Pseudomonas putida mt-2 (Pp) and Leptothrix cholodnii SP-6 (Lc). In both organisms, VPH is in a complex with the preceding enzyme in the pathway, 4-oxalocrotonate decarboxylase (4-OD). In D2O, a deuteron is incorporated stereospecifically at the C-3 and C-5 positions of product by both Pp and Lc enzymes. Accordingly, the complexes generate (3S,5S)-3,5-[di-D]-2-keto-4S-hydroxyhexanoate and (3S,5R)-3,5-[di-D]-2-keto-4R-hydroxy-5-chloropentanoate (4R and 5R due to a priority numbering change). The substitution at C-5 (CH3 or Cl) or the source of the enzyme (Pp or Lc) does not change the stereochemical outcome. One mechanism that can account for the results is the ketonization of the 5-substituted dienol to the α,β-unsaturated ketone (placing a deuteron at C-5 in D2O), followed by the conjugate addition of water (placing a deuteron at C-3). The stereochemical outcome for VPH (from Pp and Lc) is the same as that reported for a related enzyme, 2-oxo-hept-4-ene-1,7-dioate hydratase, from Escherichia coli C. The combined observations suggest similar mechanisms for these three enzymes that could possibly be common to this group of enzymes.
Collapse
Affiliation(s)
- William H Johnson
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and ‡Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Tyler M M Stack
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and ‡Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Stephanie M Taylor
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and ‡Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Elizabeth A Burks
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and ‡Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and ‡Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| |
Collapse
|
4
|
Nešvera J, Rucká L, Pátek M. Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:107-60. [PMID: 26505690 DOI: 10.1016/bs.aambs.2015.06.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.
Collapse
Affiliation(s)
- Jan Nešvera
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Lenka Rucká
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| |
Collapse
|
5
|
Izumi A, Rea D, Adachi T, Unzai S, Park SY, Roper DI, Tame JRH. Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli. J Mol Biol 2007; 370:899-911. [PMID: 17559873 DOI: 10.1016/j.jmb.2007.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 05/01/2007] [Accepted: 05/03/2007] [Indexed: 10/23/2022]
Abstract
HpcG catalyses the hydration of a carbon-carbon double bond without the aid of any cofactor other than a simple divalent metal ion such as Mg(2+). Since the substrate has a nearby carbonyl group, it is believed that it first isomerises to form a pair of conjugated double bonds in the enol tautomer before Michael addition of water. Previous chemical studies of the reaction, and that of the related enzyme MhpD, have failed to provide a clear picture of the mechanism. The substrate itself is unstable, preventing co-crystallisation or soaking of crystals, but oxalate is a strong competitive inhibitor. We have solved the crystal structure of the protein in the apo form, and with magnesium and oxalate bound. Modelling substrate into the active site suggests the attacking water molecule is not part of the metal coordination shell, in contrast to a previous proposal. Our model suggests that geometrically strained cis isomer intermediates do not lie on the reaction pathway, and that separate groups are involved in the isomerisation and hydration steps.
Collapse
Affiliation(s)
- Atsushi Izumi
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan
| | | | | | | | | | | | | |
Collapse
|
6
|
Adachi T, Izumi A, Rea D, Park SY, Tame JRH, Roper DI. Expression, purification and crystallization of 2-oxo-hept-4-ene-1,7-dioate hydratase (HpcG) from Escherichia coli C. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1010-2. [PMID: 17012798 PMCID: PMC2225172 DOI: 10.1107/s1744309106035901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 09/05/2006] [Indexed: 12/02/2022]
Abstract
The gene encoding 2-oxo-hept-3-ene-1,7-dioic acid (OHED) hydratase (HpcG) was cloned into the high-expression plasmid pET26b and overexpressed in Escherichia coli BL21(DE3). The enzyme was purified in three steps to greater than 95% purity prior to crystallization. Crystals were obtained by the hanging-drop vapour-diffusion method at 277 K in a number of screening conditions. Crystals measuring up to 1.5 mm in their longest dimension were grown from solutions containing polyethylene glycol 20 000. The crystals belonged to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = 136, b = 136, c = 192 A. A complete data set was collected to 2.1 A from a single cryocooled crystal at 100 K using synchrotron radiation.
Collapse
Affiliation(s)
- Tomoko Adachi
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
| | - Atsushi Izumi
- Division of Protein Design, Yokohama City University, Suehiro 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Dean Rea
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
| | - Sam-Yong Park
- Division of Protein Design, Yokohama City University, Suehiro 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Jeremy R. H. Tame
- Division of Protein Design, Yokohama City University, Suehiro 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - David I. Roper
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
| |
Collapse
|
7
|
Kimbara K. Recent Developments in the Study of Microbial Aerobic Degradation of Polychlorinated Biphenyls. Microbes Environ 2005. [DOI: 10.1264/jsme2.20.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|