Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes

ISME J. 2019 Aug;13(8):2005-2017. doi: 10.1038/s41396-019-0414-z. Epub 2019 Apr 5.

Abstract

Lanthanides (Ln3+), known as rare earth elements, have recently emerged as enzyme cofactors, contrary to prior assumption of their biological inertia. Several bacterial alcohol dehydrogenases have been characterized so far that depend on Ln3+ for activity and expression, belonging to the methanol dehydrogenase clade XoxF and the ethanol dehydrogenase clade ExaF/PedH. Here we compile an inventory of genes potentially encoding Ln3+-dependent enzymes, closely related to the previously characterized XoxF and ExaF/PedH enzymes. We demonstrate their wide distribution among some of the most numerically abundant and environmentally important taxa, such as the phylogenetically disparate rhizobial species and metabolically versatile bacteria inhabiting world's oceans, suggesting that reliance on Ln3+-mediated biochemistry is much more widespread in the microbial world than previously assumed. Through protein expression and analysis, we here more than double the extant collection of the biochemically characterized Ln3+-dependent enzymes, demonstrating a range of catalytic properties and substrate and cofactor specificities. Many of these enzymes reveal propensity for oxidation of methanol. This observation, in combination with genome-based reconstruction of methylotrophy pathways for select species suggests a much wider occurrence of this metabolic capability among bacterial species, and thus further suggests the importance of methylated compounds as parts of the global carbon cycling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alcohol Dehydrogenase / genetics
  • Alcohol Dehydrogenase / metabolism*
  • Bacteria / classification
  • Bacteria / enzymology*
  • Bacteria / metabolism
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Coenzymes / metabolism*
  • Lanthanoid Series Elements / metabolism*
  • Methanol / metabolism
  • Phylogeny

Substances

  • Bacterial Proteins
  • Coenzymes
  • Lanthanoid Series Elements
  • Alcohol Dehydrogenase
  • Methanol