Phylogenetic characterization and novelty of organic sulphur metabolizing genes of Rhodococcus spp. (Eu-32)
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Rhodococcus spp. (Eu-32) has the unique ability to metabolize organic sulphur containing compounds like dibenzothiophene through an extended sulphur specific pathway (Akhtar et al., in FEMS Microbiol Lett 301:95–102, 2009). Efforts were made to isolate and characterize the presumed desulphurizing genes (dszABC) involved in the sulphur specific pathway of isolate Eu-32 by employing standard and degenerate polymerase chain reaction primers. The partial dszA gene sequence of isolate Eu-32 showed 92 % sequence identity with a putative FMNH-2 dependent monooxygenase of Rhodococcus erythropolis PR4. The dszC gene sequence showed 99 % homology with the dibenzothiophene monooxygenase desulphurizing enzyme of another Rhodococcus species. The dszB gene was not unambiguously identified. A phylogenetic analysis by maximum likelihood method of the 16S rRNA gene and deduced DszA and C amino acid sequences suggest that horizontal gene transfer events might have taken place during the evolution of desulphurizing genes of Rhodococcus spp. (Eu-32).
KeywordsBiodesulphurization dszABC genes Horizontal gene transfer (HGT) PCR amplification Phylogenetic analysis Rhodococcus spp. (Eu-32)
We are thankful to Ministry of Science and Technology, Pakistan, Higher Education Commission, Pakistan and University of Leicester, UK for financial support and cooperation. We thank Dr. John Kilbane of Illinois Institute of Technology, USA for providing a culture of Rhodococcus erythropolis IGTS8 as a gift and other technical help.
Supplementary Fig. 1—Multiple alignment of the amino acid sequence of the desulphurizing enzyme, DBTO2 monooxygenase (DszA) from various desulphurizing bacteria. Amino acid residues conserved in all members are indicated by white letters in black boxes with an arrow sign. The regions that were diagnostic for the PCR amplification of dszA gene are shown in rectangle boxes. DszA_IGTS8, Rhodococcus erythropolis IGTS8 (AAA99482); DszA_1B, Gordonia alkinovorans strain 1B (AAT78716); BdsA_WUS2B, Bacillus subtilis WU-S2B (BAC20180) and TdsA_A11-2, Paenibacillus sp. A11-2 (BAA94831)
Supplementary Fig. 2—Multiple alignment of the amino acid sequence of the desulphurizing enzyme, DBTO monooxygenase (DszC), from various desulphurizing bacteria. Amino acid residues identical in all members are indicated by white letters in black boxes. The regions that were diagnostic for the PCR amplification of dszC gene are shown in rectangle boxes. DszC_IGTS8, Rhodococcus erythropolis IGTS8 (AAA99484); DszC_1B, Gordonia alkinovorans strain 1B (AAT78718); BdsC_WUS2B, Bacillus subtilis WU-S2B (BAC20182) and TdsC_A11-2, Paenibacillus sp. A11-2 (BAA94833).
Supplementary Fig. 3—Multiple alignment of the amino acid sequence of the desulphurizing enzyme, HPBS desulfinase (DszB), from various desulphurizing bacteria. Amino acid residues identical in all members are indicated by white letters in black boxes with an arrow sign. DszB_IGTS8, Rhodococcus erythropolis IGTS8 (AAA99483); DszB_1B, Gordonia alkinovorans strain 1B (AAT78717); BdsB_WUS2B, Bacillus subtilis WU-S2B (BAC20181) and TdsB_A11-2, Paenibacillus sp. A11-2 (BAA94832).
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