Characterization of Substrate, Cosubstrate, and Product Isotope Effects Associated With Enzymatic Oxygenations of Organic Compounds Based on Compound-Specific Isotope Analysis

Sarah G. Pati, Hans Peter E. Kohler, Thomas B. Hofstetter

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Pages291-329
Number of pages39
DOIs
StatePublished - 2017

Publication series

NameMethods in Enzymology
Volume596
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Bibliographical note

Funding Information:
This work was supported by the Swiss National Science Foundation (grants no. 206021-139’111/1) and the Swiss-Polish Research Collaboration (PSRP-025/200).

Keywords

  • Apparent kinetic isotope effects
  • Compound-specific isotope analysis
  • Enzyme assays
  • Isotope ratio mass spectrometry
  • Nitrobenzene dioxygenase
  • Oxygen activation
  • Pollutant biodegradation
  • Rieske non-heme ferrous iron oxygenase

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