Characterization of a phylogenetically distinct extradiol dioxygenase involved in the bacterial catabolism of lignin-derived aromatic compounds

Laura E. Navas, Michael Zahn, Harbir Bajwa, Jason C. Grigg, Megan E. Wolf, Anson C.K. Chan, Michael E.P. Murphy, John McGeehan, Lindsay Eltis*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

The actinobacterium Rhodococcus jostii RHA1 grows on a remarkable variety of aromatic compounds and has been studied for applications ranging from the degradation of polychlorinated biphenyls to the valorization of lignin, an underutilized component of biomass. In RHA1, the catabolism of two classes of lignin-derived compounds, alkylphenols and alkylguaiacols, involves a phylogenetically distinct extradiol dioxygenase, AphC, previously misannotated as BphC, an enzyme involved in biphenyl catabolism. To better understand the role of AphC in RHA1 catabolism, we first showed that purified AphC had highest apparent specificity for 4-propylcatechol (kcat/KM ∼106 M-1 s-1), and its apparent specificity for 4-alkylated substrates followed the trend for alkylguaiacols: propyl > ethyl > methyl > phenyl > unsubstituted. We also show AphC only poorly cleaved 3-phenylcatechol, the preferred substrate of BphC. Moreover, AphC and BphC cleaved 3- and 4-phenylcatechols with different regiospecificities, likely due to the substrates’ binding mode. A crystallographic structure of the AphC·4-ethylcatechol binary complex to 1.59 Å resolution revealed that the catechol is bound to the active site iron in a bidentate manner and that the substrate’s alkyl side chain is accommodated by a hydrophobic pocket. Finally, we show RHA1 grows on a mixture of 4-ethylguaiacol and guaiacol, simultaneously catabolizing these substrates through meta- and ortho-cleavage pathways, respectively, suggesting that the specificity of AphC helps to prevent the routing of catechol through the Aph pathway. Overall, this study contributes to our understanding of the bacterial catabolism of aromatic compounds derived from lignin, and the determinants of specificity in extradiol dioxygenases.
Original languageEnglish
JournalThe Journal of Biological Chemistry
Early online date26 Mar 2022
DOIs
Publication statusEarly online - 26 Mar 2022

Keywords

  • bacterial metabolism
  • actinobacteria
  • metalloenzyme
  • biotechnology
  • enzyme structure
  • lignin valorization
  • biocatalysis
  • guaiacol

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