Limited aromatic pathway genes diversity amongst aromatic compound degrading soil bacterial isolates

Abstract

Identification and characterization of novel genes belonging to microbial aromatic biodegradation pathway is of great importance as they have been proven versatile biocatalysts. In this study, the selection of 19 environmental bacterial isolates capable to degrade a wide range of aromatic compounds has been screened for the presence of five genes from the lower and the upper aromatic biodegradation pathway using PCR methodology. In the case of 4-oxalocrotonate tautomerase and toluene dioxygenases, although present in the most of environmental isolates, very limited diversity of the genes has been encountered. Highly conserved sequences of these genes in environmental samples revealed high homology with gene sequences of the characterized corresponding genes from Pseudomonas putida species. The screen using degenerate primers based on known catechol-and naphthalene dioxygenases sequences resulted in a limited number of amplified fragments. Only two catechol 2,3-dioxygenase from two Bacillus isolates were amplified and showed no significant similarities with dioxygenases from characterized organisms, but 80-90% identities with partial catechol 2,3-dioxygenase sequences from uncultured organisms. Potentially three novel catechol 1,2-dioxygenases were identified from Bacillus sp. TN102, Gordonia sp. TN103 and Rhodococcus sp. TN112. Highly homologous tautomerase and toluene dioxygenases amongst environmental samples isolated from the contaminated environment suggested horizontal gene transfer while limited success in PCR detection of the other three genes indicates that these isolates may still be a source of novel genes. [Projekat Ministarstva nauke Republike Srbije, br. 173048]

Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

“…7,8 Recently, research on the biodegradation of aromatic hydrocarbons has intensied, including screening for aromatic hydrocarbon-degrading strains, 9 degradation characteristics, 10 metabolic pathways, 11 and degradation mechanisms 12 and the construction of efficient genetically engineered bacteria. 13 Studies reported that a variety of microbial strains to degrade different types of aromatic hydrocarbons in petroleum have been screened out. 14,15 However, some strains barely adapt to the environment and reproduce at a slow rate, so it is difficult to achieve a degradation rate of aromatic hydrocarbons that meets processing requirements.…”