alkB homologs in thermophilic bacteria of the genus Geobacillus

Screening for alkane hydroxylase genes ( alk B) was performed in thermophilic aerobic bacteria of the genus Geobacillus . Total DNAs were isolated from the biomass of 11 strains grown on a mixture of saturated C 10 –C 20 hydrocarbons. Fragments of alk B genes were amplified by PCR with degenerate oligonucleotide primers, and the PCR products were cloned and sequenced. For the first time, a set of alk B gene homologs was detected in the genomes of thermophilic bacteria. The strains each contained three to six homologs, of which only two were common for all of the strains. Phylogenetic analysis of the nucleotide sequences and the deduced amino acid sequences showed that six of the variants revealed in Geobacillus were closely related to alk B4, alk B3, and alk B2, found in Rhodococcus erythropolis strains NRRL B-16531 and Q15. All variants of alk B sequences were unique. Analysis of the GC composition showed that the Geobacillus alk B homologs are closer to Rhodococcus than to Geobacillus chromosomal DNA. It was assumed that the alk B genes were introduced in the Geobacillus genome via interspecific horizontal transfer and that Rhodococcus or other representatives of Actinobacteria served as donors. Analysis of the codon usage in the fragments of alk B genes confirmed the suggestion that the pool of these genes is common to the majority of Gram-positive and certain Gram-negative bacteria. The formation of a set of several alk B homologs in a genome of a particular microorganism may result from free gene exchange within this pool.