1
|
Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
Collapse
Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
2
|
Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
Collapse
Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
3
|
Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
Collapse
Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
4
|
Ma LL, Yang GP, Li GP, Zhang PF, Jin J, Wang Y, Wang JM, Wang YY. Luminescence modulation, near white light emission, selective luminescence sensing, and anticounterfeiting via a series of Ln-MOFs with a π-conjugated and uncoordinated lewis basic triazolyl ligand. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01100b] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of Ln-MOFs with π-conjugated and uncoordinated lewis basic triazolyl ligand have luminescence modulation, near white light emission, selective luminescence sensing, and anticounterfeiting.
Collapse
Affiliation(s)
- Lu-Lu Ma
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Guo-Ping Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Gao-Peng Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Peng-Feng Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Jing Jin
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Yao Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Jiao-Min Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| | - Yao-Yu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education
- Shaanxi Key Laboratory of Physico-Inorganic Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
| |
Collapse
|
5
|
Xiao X, Ma XL, Wang LG, Long F, Li TT, Zhou XT, Liu H, Wu LJ, Yu HQ. Anaerobic reduction of high-polarity nitroaromatic compounds by electrochemically active bacteria: Roles of Mtr respiratory pathway, molecular polarity, mediator and membrane permeability. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115943. [PMID: 33158624 DOI: 10.1016/j.envpol.2020.115943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Electrochemically active bacteria (EAB) are effective for the bioreduction of nitroaromatic compounds (NACs), but the exact reduction mechanisms are unclear yet. Therefore, 3-nitrobenzenesulfonate (NBS) was used to explore the biodegradation mechanism of NACs by EAB. Results show that NBS could be anaerobically degraded by Shewanella oneidensis MR-1. The generation of aminoaromatic compounds was accompanied with the NBS reduction, indicating that NBS was biodegraded via reductive approach by S. oneidensis MR-1. The impacts of NBS concentration and cell density on the NBS reduction were evaluated. The removal of NBS depends mainly on the transmembrane electron transfer of S. oneidensis MR-1. Impairment of Mtr respiratory pathway was found to mitigate the reduction of NBS, suggesting that the anaerobic biodegradation of NBS occurred extracellularly. Knocking out cymA severely impaired the extracellular reduction ability of S. oneidensis MR-1. However, the phenotype of ΔcymA mutant could be compensated by the exogenous electron mediators, implying the trans-outer membrane diffusion of mediators into the periplasmic space. This work provides a new insight into the anaerobic reduction of aromatic contaminants by EAB.
Collapse
Affiliation(s)
- Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiao-Lin Ma
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Lu-Guang Wang
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Fei Long
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Ting-Ting Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiang-Tong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Li-Jun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Han-Qing Yu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
| |
Collapse
|
6
|
Ojeda AS, Phillips E, Mancini SA, Lollar BS. Sources of Uncertainty in Biotransformation Mechanistic Interpretations and Remediation Studies using CSIA. Anal Chem 2019; 91:9147-9153. [DOI: 10.1021/acs.analchem.9b01756] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ann Sullivan Ojeda
- Department of Earth Sciences, The University of Toronto, 22 Russell Street, Toronto, Ontario M5S 3B1, Canada
| | - Elizabeth Phillips
- Department of Earth Sciences, The University of Toronto, 22 Russell Street, Toronto, Ontario M5S 3B1, Canada
| | - Silvia A. Mancini
- Geosyntec Consultants Inc., 243 Islington Avenue #1201, Etobicoke, Ontario M8X 1Y9, Canada
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, The University of Toronto, 22 Russell Street, Toronto, Ontario M5S 3B1, Canada
| |
Collapse
|
7
|
Berens MJ, Ulrich BA, Strehlau JH, Hofstetter TB, Arnold WA. Mineral identity, natural organic matter, and repeated contaminant exposures do not affect the carbon and nitrogen isotope fractionation of 2,4-dinitroanisole during abiotic reduction. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:51-62. [PMID: 30484795 DOI: 10.1039/c8em00381e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The recent development of insensitive munitions, such as 2,4-dinitroanisole (DNAN), as components of military explosives has generated concern for potential subsurface contamination and created a need to fully characterize their transformation processes. Compound specific isotope analysis (CSIA) has proven to be a useful means of assessing transformation pathways according to characteristic stable isotope fractionation patterns. The C and N isotope fractionation of DNAN associated with abiotic and enzymatic hydrolysis was recently assessed. The extent to which DNAN isotope fractionation will be affected by other potentially competing transformation pathways known for nitroaromatic compounds (e.g., reduction) and if previous knowledge can be extrapolated to other environmental matrices remains to be understood. Here, we investigated the C and N isotope fractionation and reaction rate constants of DNAN during abiotic reduction mediated by mineral-associated Fe(ii) species as a function of mineral type, natural organic matter presence, and repeated exposures to DNAN. Though rate constants varied, N and C apparent kinetic isotope effects (AKIEs) remained consistent across all experiments (averaged values of 15N-AKIE = 1.0317 ± 0.0064 and 13C-AKIE = 1.0008 ± 0.0005) and revealed significant 15N- and minimal 13C-enrichment in agreement with previous work on nitroaromatic compounds. Moreover, the observed fractionation was clearly distinct from trends for abiotic and enzymatic hydrolysis. This study provides a strengthened basis for the use of CSIA as a robust tool for monitoring DNAN degradation in complex environmental matrices as a component of future remediation efforts.
Collapse
Affiliation(s)
- Matthew J Berens
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, 500 Pillsbury Drive SE, Minneapolis, MN 55455-0116, USA.
| | | | | | | | | |
Collapse
|
8
|
Passeport E, Zhang N, Wu L, Herrmann H, Sherwood Lollar B, Richnow HH. Aqueous photodegradation of substituted chlorobenzenes: Kinetics, carbon isotope fractionation, and reaction mechanisms. WATER RESEARCH 2018; 135:95-103. [PMID: 29459118 DOI: 10.1016/j.watres.2018.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 06/08/2023]
Abstract
Substituted chlorobenzenes are the basic substructure of many surface water contaminants. In this study, the isotope fractionation and reaction mechanisms involved during the aqueous direct and indirect photodegradation of CH3-, Cl-, and NO2- substituted chlorobenzenes were investigated in laboratory experiments. Only 4-nitrochlorobenzene showed slow but isotopically fractionating direct photolysis. During indirect photodegradation using UV/H2O2-generated OH radicals, the pseudo first-order reaction rate constants increased in the order of the NO2- < Cl- < CH3- substituted chlorobenzenes. The most pronounced carbon enrichment factors were observed for nitrochlorobenzenes (up to -4.8 ± 0.5‰), whereas the lowest were for chlorotoluenes (≤-1.0 ± 0.1‰). As the substituents became more electron-withdrawing, the activation energy barrier increased, leading to slower reaction rates, and the transition state changed to a more symmetrical or less reactant-like structure, resulting in larger apparent kinetic isotope effects. The results suggest that the rate-determining step in the reaction with OH radicals was the addition of the electrophile to the benzene ring. Even though further research is needed to quantify isotope fractionation during other transformation processes, these results showed evidence that compound specific isotope analysis can be used as a diagnostic tool for the fate of substituted chlorobenzenes in water.
Collapse
Affiliation(s)
- Elodie Passeport
- Department of Earth Sciences, University of Toronto, 22 Russell Street, Toronto, ON M5S 3B1, Canada.
| | - Ning Zhang
- Department of Isotope Biogeochemistry, Helmholtz Center for Environmental Research UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Langping Wu
- Department of Isotope Biogeochemistry, Helmholtz Center for Environmental Research UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hartmut Herrmann
- TROPOS Leibniz Institute for Tropospheric Research, Atmospheric Chemistry Department (ACD), Permoserstrasse 15, 04318 Leipzig, Germany
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Russell Street, Toronto, ON M5S 3B1, Canada
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Center for Environmental Research UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| |
Collapse
|
9
|
Spahr S, von Gunten U, Hofstetter TB. Carbon, Hydrogen, and Nitrogen Isotope Fractionation Trends in N-Nitrosodimethylamine Reflect the Formation Pathway during Chloramination of Tertiary Amines. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:13170-13179. [PMID: 29032675 DOI: 10.1021/acs.est.7b03919] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Assessing the precursors and reactions leading to the carcinogenic N-nitrosodimethylamine (NDMA) during drinking water disinfection is a major challenge. Here, we investigate whether changes of 13C/12C, 2H/1H, and 15N/14N ratios of NDMA give rise to isotope fractionation trends that can be used to infer NDMA formation pathways. We carried out compound-specific isotope analysis (CSIA) of NDMA during chloramination of four tertiary amines that produce NDMA at high yields, namely ranitidine, 5-(dimethylaminomethyl)furfuryl alcohol, N,N-dimethylthiophene-2-methylamine, and N,N-dimethylbenzylamine. Carbon and hydrogen isotope ratios of NDMA function as fingerprints of the N(CH3)2 moiety and exhibit only minor isotope fractionation during the disinfection process. Nitrogen isotope ratios showed that NH2Cl is the source of the N atom of the nitroso group. The large enrichment of 15N in NDMA was indicative of the isotope effects pertinent to bond-cleavage and bond-formation reactions during chloramination of the tertiary amines. Correlation of δ15N versus δ13C values of NDMA resulted in trend lines that were not affected by the type of tertiary amine and treatment conditions, suggesting that the observed C and N isotope fractionation in NDMA may be diagnostic for NDMA precursors and formation pathways during chloramination.
Collapse
Affiliation(s)
- Stephanie Spahr
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Federale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Urs von Gunten
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Federale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich , CH-8092 Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich , CH-8092 Zürich, Switzerland
| |
Collapse
|
10
|
Pati SG, Kohler HPE, Hofstetter TB. Characterization of Substrate, Cosubstrate, and Product Isotope Effects Associated With Enzymatic Oxygenations of Organic Compounds Based on Compound-Specific Isotope Analysis. Methods Enzymol 2017; 596:291-329. [PMID: 28911775 DOI: 10.1016/bs.mie.2017.06.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Enzymatic oxygenations are among the most important biodegradation and detoxification reactions of organic pollutants. In the environment, however, such natural attenuation processes are extremely difficult to monitor. Changes of stable isotope ratios of aromatic pollutants at natural isotopic abundances serve as proxies for isotope effects associated with oxygenation reactions. Such isotope fractionations offer new avenues for revealing the pathway and extent of pollutant transformation and provide new insights into the mechanisms of catalysis by Rieske non-heme ferrous iron oxygenases. Based on compound-specific C, H, N, and O isotope analysis, we present a comprehensive methodology with which isotope effects can be derived from the isotope fractionation measured in substrates, the cosubstrate O2, and organic oxygenation products. We use dioxygenation of nitrobenzene and 2-nitrotoluene by nitrobenzene dioxygenase as illustrative examples to introduce different mathematical procedures for deriving apparent substrate and product isotope effects. We present two experimental approaches to control reactant and product turnover for isotope fractionation analysis in experimental systems containing purified enzymes, E. coli clones, and pure strains of environmental microorganisms. Finally, we present instrumental procedures and sample treatment instructions for analysis of C, H, and N isotope analysis in organic compounds and O isotope analysis in aqueous O2 by gas and liquid chromatography coupled to isotope ratio mass spectrometry.
Collapse
Affiliation(s)
- Sarah G Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
11
|
Klajman K, Ciepielowski G, Kamiński R, Adamczyk P, Paneth P. Resolving Discrepancy between Theory and Experiment in 4-Nitrotoluene Oxidation. J Phys Chem A 2017; 121:6638-6645. [PMID: 28806085 DOI: 10.1021/acs.jpca.7b05474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have performed calculations of possible oxidation pathways of 4-nitrotoluene (4NT) by permanganate anion and evaluated relative contributions of oxidation of the methyl group and aromatic ring. Although a few theory levels matched the experimental results obtained by compound specific isotope analysis (CSIA) for 4NT, they failed in reproducing results for other nitrotoluene derivatives studied previously [Wijker, R.S.; Adamczyk, P.; Bolotin, J.; Paneth, P.; Hofstetter, T.B. Environ. Sci. Technol., 2013, 47, 13459-13468]. This discrepancy prompted us to reevaluate the experimental isotopic fractionation of carbon and hydrogen for 4NT on which the relative contributions of the oxidation channels has been based. Using position specific isotope analysis (PSIA) for hydrogen isotopic fractionation we have found that the previously determined value was incorrect. Reexamination of theory levels that are in agreement with these new findings indicated that while a better agreement for this particular case can be reached, overall, the previously used B3LYP functional expressed in the 6-31+G(d,p) basis set with inclusion of the polarized continuum model (PCM) of aqueous solution remains the theoretical level of choice in modeling oxidation of nitrotoluene derivatives by permanganate.
Collapse
|
12
|
Tea I, Tcherkez G. Natural Isotope Abundance in Metabolites: Techniques and Kinetic Isotope Effect Measurement in Plant, Animal, and Human Tissues. Methods Enzymol 2017; 596:113-147. [PMID: 28911768 DOI: 10.1016/bs.mie.2017.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The natural isotope abundance in bulk organic matter or tissues is not a sufficient base to investigate physiological properties, biosynthetic mechanisms, and nutrition sources of biological systems. In fact, isotope effects in metabolism lead to a heterogeneous distribution of 2H, 18O, 13C, and 15N isotopes in metabolites. Therefore, compound-specific isotopic analysis (CSIA) is crucial to biological and medical applications of stable isotopes. Here, we review methods to implement CSIA for 15N and 13C from plant, animal, and human samples and discuss technical solutions that have been used for the conversion to CO2 and N2 for IRMS analysis, derivatization and isotope effect measurements. It appears that despite the flexibility of instruments used for CSIA, there is no universal method simply because the chemical nature of metabolites of interest varies considerably. Also, CSIA methods are often limited by isotope effects in sample preparation or the addition of atoms from the derivatizing reagents, and this implies that corrections must be made to calculate a proper δ-value. Therefore, CSIA has an enormous potential for biomedical applications, but its utilization requires precautions for its successful application.
Collapse
Affiliation(s)
- Illa Tea
- Research School of Biology, Australian National University, Canberra, ACT, Australia; Cancer Metabolism and Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia; EBSI Team, CEISAM, University of Nantes-CNRS UMR 6230, Nantes, France
| | - Guillaume Tcherkez
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| |
Collapse
|
13
|
Wijker RS, Zeyer J, Hofstetter TB. Isotope fractionation associated with the simultaneous biodegradation of multiple nitrophenol isomers by Pseudomonas putida B2. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:775-784. [PMID: 28470308 DOI: 10.1039/c6em00668j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Quantifying the extent of biodegradation of nitroaromatic compounds (NACs) in contaminated soils and sediments is challenging because of competing oxidative and reductive reaction pathways. We have previously shown that the stable isotope fractionation of NACs reveals the routes of degradation even if it is simultaneously caused by different bacteria. However, it is unclear whether compound-specific isotope analysis (CSIA) can be applied in situations where multiple pollutants are biodegraded by only one microorganism under multi-substrate conditions. Here we examined the C and N isotope fractionation of 2-nitrophenol (2-NP) and 3-nitrophenol (3-NP) during biodegradation by Pseudomonas putida B2 through monooxygenation and partial reductive pathways, respectively, in the presence of single substrates vs. binary substrate mixtures. Laboratory experiments showed that the reduction of 3-NP by Pseudomonas putida B2 is associated with large N and minor C isotope fractionation with C and N isotope enrichment factors, εC and εN, of -0.3 ± 0.1‰ and -22 ± 0.2‰, respectively. The opposite isotope fractionation trends were found for 2-NP monooxygenation. In the simultaneous presence of 2-NP and 3-NP, 2-NP is biodegraded at identical rate constants and εC and εN values (-1.0 ± 0.1‰ and -1.3 ± 0.2‰) to those found for the monooxygenation of 2-NP in single substrate experiments. While the pathway and N isotope fractionation of 3-NP reduction (εN = -24 ± 1.1‰) are independent of the presence of 2-NP, intermediates of 2-NP monooxygenation interfere with 3-NP reduction. Because neither pH, substrate uptake, nor aromatic substituents affected the kinetic isotope effects of nitrophenol biodegradation, our study illustrates that CSIA provides robust scientific evidence for the assessment of natural attenuation processes.
Collapse
Affiliation(s)
- Reto S Wijker
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland.
| | | | | |
Collapse
|
14
|
Optimized degradation removal of 2-nitrotoluene by combination of cathodic reduction and electro-oxidation process. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
15
|
Pati SG, Kohler HPE, Pabis A, Paneth P, Parales RE, Hofstetter TB. Substrate and Enzyme Specificity of the Kinetic Isotope Effects Associated with the Dioxygenation of Nitroaromatic Contaminants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6708-16. [PMID: 26895026 DOI: 10.1021/acs.est.5b05084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Compound-specific isotope analysis (CSIA) is a promising approach for tracking biotransformation of organic pollutants, but isotope fractionation associated with aromatic oxygenations is only poorly understood. We investigated the dioxygenation of a series of nitroaromatic compounds to the corresponding catechols by two enzymes, namely, nitrobenzene and 2-nitrotoluene dioxygenase (NBDO and 2NTDO) to elucidate the enzyme- and substrate-specificity of C and H isotope fractionation. While the apparent (13)C- and (2)H-kinetic isotope effects of nitrobenzene, nitrotoluene isomers, 2,6-dinitrotoluene, and naphthalene dioxygenation by NBDO varied considerably, the correlation of C and H isotope fractionation revealed a common mechanism for nitrobenzene and nitrotoluenes. Similar observations were made for the dioxygenation of these substrates by 2NTDO. Evaluation of reaction kinetics, isotope effects, and commitment-to-catalysis based on experiment and theory showed that rates of dioxygenation are determined by the enzymatic O2 activation and aromatic C oxygenation. The contribution of enzymatic O2 activation to the reaction rate varies for different nitroaromatic substrates of NBDO and 2NTDO. Because aromatic dioxygenation by nonheme iron dioxygenases is frequently the initial step of biodegradation, O2 activation kinetics may also have been responsible for the minor isotope fractionation reported for the oxygenation of other aromatic contaminants.
Collapse
Affiliation(s)
- Sarah G Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich , 8092 Zürich, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Anna Pabis
- Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, University of California , Davis, California 95616, United States
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich , 8092 Zürich, Switzerland
| |
Collapse
|
16
|
Ratti M, Canonica S, McNeill K, Bolotin J, Hofstetter TB. Isotope Fractionation Associated with the Indirect Photolysis of Substituted Anilines in Aqueous Solution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12766-12773. [PMID: 26418612 DOI: 10.1021/acs.est.5b03119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Organic micropollutants containing aniline substructures are susceptible to different light-induced transformation processes in aquatic environments and water treatment operations. Here, we investigated the magnitude and variability of C and N isotope fractionation during the indirect phototransformation of four para-substituted anilines in aerated aqueous solutions. The model photosensitizers, namely 9,10-anthraquinone-1,5-disulfonate and methylene blue, were used as surrogates for dissolved organic matter chromophores generating excited triplet states in sunlit surface waters. The transformation of aniline, 4-CH3-, 4-OCH3-, and 4-Cl-aniline by excited triplet states of the photosensitizers was associated with inverse and normal N isotope fractionation, whereas C isotope fractionation was negligible. The apparent 15N kinetic isotope effects (AKIE) were almost identical for both photosensitizers, increased from 0.9958±0.0013 for 4-OCH3-aniline to 1.0035±0.0006 for 4-Cl-aniline, and correlated well with the electron donating properties of the substituent. N isotope fractionation is pH-dependent in that H+ exchange reactions dominate below and N atom oxidation processes above the pKa value of the substituted aniline's conjugate acid. Correlations of C and N isotope fractionation for indirect phototransformation were different from those determined previously for the direct photolysis of chloroanilines and offer new opportunities to distinguish between abiotic degradation pathways.
Collapse
Affiliation(s)
- Marco Ratti
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich , CH-8092 Zürich, Switzerland
| | - Silvio Canonica
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich , CH-8092 Zürich, Switzerland
| | - Jakov Bolotin
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich , CH-8092 Zürich, Switzerland
| |
Collapse
|
17
|
Birkigt J, Gilevska T, Ricken B, Richnow HH, Vione D, Corvini PFX, Nijenhuis I, Cichocka D. Carbon Stable Isotope Fractionation of Sulfamethoxazole during Biodegradation by Microbacterium sp. Strain BR1 and upon Direct Photolysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6029-6036. [PMID: 25906077 DOI: 10.1021/acs.est.5b00367] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Carbon isotope fractionation of sulfamethoxazole (SMX) during biodegradation by Microbacterium sp. strain BR1 (ipso-hydroxylation) and upon direct photolysis was investigated. Carbon isotope signatures (δ(13)C) of SMX were measured by LC-IRMS (liquid chromatography coupled to isotope ratio mass spectrometry). A new LC-IRMS method for the SMX metabolite, 3-amino-5-methylisoxazole (3A5MI), was established. Carbon isotope enrichment factors for SMX (ε(C)) were -0.6 ± 0.1‰ for biodegradation and -2.0 ± 0.1‰ and -3.0 ± 0.2‰ for direct photolysis, at pH 7.4 and pH 5, respectively. The corresponding apparent kinetic isotope effects (AKIE) for ipso-hydroxylation were 1.006 ± 0.001; these fall in the same range as AKIE in previously studied hydroxylation reactions. The differences in SMX and 3A5MI fractionation upon biotic and abiotic degradation suggest that compound specific stable isotope analysis (CSIA) is a suitable method to distinguish SMX reaction pathways. In addition, the study revealed that the extent of isotope fractionation during SMX photolytic cleavage is pH-dependent.
Collapse
Affiliation(s)
- Jan Birkigt
- †Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Saxony, Germany
| | - Tetyana Gilevska
- †Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Saxony, Germany
| | - Benjamin Ricken
- ‡Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Basel-Landschaft, Switzerland
| | - Hans-Hermann Richnow
- †Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Saxony, Germany
| | - Davide Vione
- §Department of Chemistry, University of Torino, 10125 Torino, Torino, Italy
| | - Philippe F-X Corvini
- ‡Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Basel-Landschaft, Switzerland
| | - Ivonne Nijenhuis
- †Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Saxony, Germany
| | - Danuta Cichocka
- ‡Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Basel-Landschaft, Switzerland
| |
Collapse
|
18
|
Ratti M, Canonica S, McNeill K, Erickson PR, Bolotin J, Hofstetter TB. Isotope fractionation associated with the direct photolysis of 4-chloroaniline. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4263-4273. [PMID: 25719866 DOI: 10.1021/es505784a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Compound-specific isotope analysis is a useful approach to track transformations of many organic soil and water pollutants. Applications of CSIA to characterize photochemical processes, however, have hardly been explored. In this work, we systematically studied C and N isotope fractionation associated with the direct photolysis of 4-Cl-aniline used as a model compound for organic micropollutants that are known to degrade via photochemical processes. Laboratory experiments were carried out at an irradiation wavelength of 254 nm over the pH range 2.0 to 9.0 as well as in the presence of Cs(+) as a quencher of excited singlet 4-Cl-aniline at pH 7.0 and 9.0. We observed considerable variation of C and N isotope enrichment factors, ϵC and ϵN, between -1.2 ± 0.2‰ to -2.7 ± 0.2‰ for C and -0.6 ± 0.2‰ to -9.1 ± 1.6‰ for N, respectively, which could not be explained by the speciation of 4-Cl-aniline alone. In the presence of 1 M Cs(+), we found a marked increase of apparent (13)C-kinetic isotope effects ((13)C-AKIE) and decrease of 4-Cl-aniline fluorescence lifetimes. Our data suggest that variations of C and N isotope fractionation originate from heterolytic dechlorination of excited triplet and singlet states of 4-Cl-aniline. Linear correlations of (13)C-AKIE vs (15)N-AKIE were distinctly different for these two reaction pathways and may be explored further for the identification of photolytic aromatic dechlorination reactions.
Collapse
Affiliation(s)
- Marco Ratti
- †Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
- ‡Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092 Zürich, Switzerland
| | - Silvio Canonica
- †Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Kristopher McNeill
- ‡Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092 Zürich, Switzerland
| | - Paul R Erickson
- ‡Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092 Zürich, Switzerland
| | - Jakov Bolotin
- †Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Thomas B Hofstetter
- †Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
- ‡Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092 Zürich, Switzerland
| |
Collapse
|