D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii

J Biol Chem. 2009 Oct 2;284(40):27290-303. doi: 10.1074/jbc.M109.003814. Epub 2009 Jul 7.


The pathway of D-xylose degradation in archaea is unknown. In a previous study we identified in Haloarcula marismortui the first enzyme of xylose degradation, an inducible xylose dehydrogenase (Johnsen, U., and Schönheit, P. (2004) J. Bacteriol. 186, 6198-6207). Here we report a comprehensive study of the complete D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. The analyses include the following: (i) identification of the degradation pathway in vivo following (13)C-labeling patterns of proteinogenic amino acids after growth on [(13)C]xylose; (ii) identification of xylose-induced genes by DNA microarray experiments; (iii) characterization of enzymes; and (iv) construction of in-frame deletion mutants and their functional analyses in growth experiments. Together, the data indicate that D-xylose is oxidized exclusively to the tricarboxylic acid cycle intermediate alpha-ketoglutarate, involving D-xylose dehydrogenase (HVO_B0028), a novel xylonate dehydratase (HVO_B0038A), 2-keto-3-deoxyxylonate dehydratase (HVO_B0027), and alpha-ketoglutarate semialdehyde dehydrogenase (HVO_B0039). The functional involvement of these enzymes in xylose degradation was proven by growth studies of the corresponding in-frame deletion mutants, which all lost the ability to grow on d-xylose, but growth on glucose was not significantly affected. This is the first report of an archaeal D-xylose degradation pathway that differs from the classical D-xylose pathway in most bacteria involving the formation of xylulose 5-phosphate as an intermediate. However, the pathway shows similarities to proposed oxidative pentose degradation pathways to alpha-ketoglutarate in few bacteria, e.g. Azospirillum brasilense and Caulobacter crescentus, and in the archaeon Sulfolobus solfataricus.

MeSH terms

  • Amino Acid Sequence
  • Cell Extracts
  • Genes, Archaeal
  • Haloferax volcanii / cytology
  • Haloferax volcanii / enzymology
  • Haloferax volcanii / genetics
  • Haloferax volcanii / metabolism*
  • Hydro-Lyases / chemistry
  • Hydro-Lyases / genetics
  • Hydro-Lyases / metabolism
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Sequence Deletion
  • Xylose / metabolism*
  • Xylose / pharmacology


  • Cell Extracts
  • Xylose
  • Hydro-Lyases