The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content

Gene. 1993 Aug 16;130(1):33-9. doi: 10.1016/0378-1119(93)90343-2.


Benzene dioxygenase, catalyzing the oxidation of benzene to cis-1,2-dihydroxy-cyclohexa-3,5-diene, comprises four polypeptides that are encoded by plasmid pHMT112 of Pseudomonas putida ML2. In this study, the nucleotide (nt) sequences of four genes encoding this enzyme (bedC1C2BA) were determined, and the amino acid (aa) sequences were deduced. The sequence showed significant homology with the chromosomally encoded benzene dioxygenase and toluene dioxygenase genes (73-77% for nt and 83-99% for aa), but not the plasmid-encoded naphthalene dioxygenase genes (20-26% for nt and 32-36% for aa). A conserved motif (Cys-Xaa-His-15-to-17 aa-Cys-Xaa2-His, where Xaa is any aa), proposed to bind the Rieske-type [2Fe-2S] cluster, was identified in the deduced aa sequence of the iron-sulfur proteins. Three regions were also identified in the flavoprotein which are likely to be involved in FAD and NAD+ binding. The gene order of bedC1C2BA is consistent with most ring-hydroxylating dioxygenases isolated from Pseudomonas. However, the G+C content of 47% is in contrast to the high G+C content of the Pseudomonas chromosome (63%) and other Pseudomonas plasmids (57%), and with its unique codon usage preference this suggests that bedC1C2BA originated from a host derived from a different genus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Benzene / metabolism
  • Codon
  • Conserved Sequence
  • Cytosine / analysis
  • DNA, Bacterial / analysis*
  • Electron Transport Complex III*
  • Flavoproteins / genetics
  • Genes, Bacterial*
  • Guanine / analysis
  • Iron-Sulfur Proteins / genetics
  • Mixed Function Oxygenases / genetics*
  • Molecular Sequence Data
  • Plasmids / genetics*
  • Pseudomonas putida / enzymology*
  • Pseudomonas putida / genetics*
  • Sequence Homology, Nucleic Acid
  • Transfection


  • Codon
  • DNA, Bacterial
  • Flavoproteins
  • Iron-Sulfur Proteins
  • Rieske iron-sulfur protein
  • Guanine
  • Cytosine
  • Mixed Function Oxygenases
  • benzene 1,2-dioxygenase
  • Electron Transport Complex III
  • Benzene

Associated data

  • GENBANK/L03653
  • GENBANK/L03654
  • GENBANK/L04280
  • GENBANK/L04642
  • GENBANK/L04643
  • GENBANK/L07632
  • GENBANK/M96932
  • GENBANK/M96933
  • GENBANK/S65693
  • GENBANK/S65694
  • GENBANK/X54209