The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus

Syst Appl Microbiol. 2015 Feb;38(1):1-7. doi: 10.1016/j.syapm.2014.10.010. Epub 2014 Nov 11.


Naturally occurring and anthropogenic petroleum hydrocarbons are potential carbon sources for many bacteria. The AlkB-related alkane hydroxylases, which are integral membrane non-heme iron enzymes, play a key role in the microbial degradation of many of these hydrocarbons. Several members of the genus Rhodococcus are well-known alkane degraders and are known to harbor multiple alkB genes encoding for different alkane 1-monooxygenases. In the present study, 48 Rhodococcus strains, representing 35 species of the genus, were investigated to find out whether there was a dominant type of alkB gene widespread among species of the genus that could be used as a phylogenetic marker. Phylogenetic analysis of rhodococcal alkB gene sequences indicated that a certain type of alkB gene was present in almost every member of the genus Rhodococcus. These alkB genes were common in a unique nucleotide sequence stretch absent from other types of rhodococcal alkB genes that encoded a conserved amino acid motif: WLG(I/V/L)D(G/D)GL. The sequence identity of the targeted alkB gene in Rhodococcus ranged from 78.5 to 99.2% and showed higher nucleotide sequence variation at the inter-species level compared to the 16S rRNA gene (93.9-99.8%). The results indicated that the alkB gene type investigated might be applicable for: (i) differentiating closely related Rhodococcus species, (ii) properly assigning environmental isolates to existing Rhodococcus species, and finally (iii) assessing whether a new Rhodococcus isolate represents a novel species of the genus.

Keywords: Alkane 1-monooxygenase; Phylogenetic marker gene.; Rhodococcus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Cytochrome P-450 CYP4A / genetics*
  • Genes, Bacterial
  • Genetic Markers
  • Molecular Typing
  • Phylogeny
  • Rhodococcus / enzymology*
  • Rhodococcus / genetics
  • Sequence Analysis, DNA


  • Bacterial Proteins
  • Genetic Markers
  • Cytochrome P-450 CYP4A