Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains

Abstract

A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon–carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits.

Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel

“…Indeed, alkane monooxygenases oxidize n -alkanes to their corresponding primary alcohols. The formed alcohols are in turn oxidized by alcohol dehydrogenases that produce the corresponding alkyl aldehydes and further, carboxylic acids that enter general metabolism through the action of aldehyde dehydrogenase [ 39 , 40 , 41 ]. The alkane−1-monooxygenase enzyme, as found in this study and commonly referred to as AlkB, is encoded by the alkB gene widely spread in bacterial communities and is considered a biomarker for community remediation potential [ 35 , 42 ].…”

Insights into the Potential Role of Gordonia alkanivorans Strains in Biotechnologies

“…Previously, it was thought that thiophene catabolism in G. alkanivorans was only carried out using the dsz operon [58,59]. However, in previous studies, we have shown that there are G. alkanivorans strains that utilize thiophenes without dsz genes [60,61]. In one of the studies (2023), the ability of the strain Gordonia alkanivorans GH-1 to degrade beta-cypermethrin (β-CY), a pesticide whose breakdown products can have adverse effects on human health, was investigated.…”

“…In the subcategory «Benzoate degradation» within the «Xenobiotics biodegradation and metabolism» category, 19 KOs were identified for all strains, except for strain 134, which had 20 groups. The ability to use benzoate as a source of carbon and energy is a characteristic feature of representatives of this genus [61,85].…”

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

“…Strains used in the study were isolated from different sources and characterized as previously described ( Rhodococcus erythropolis X5 25 , Rhodococcus opacus S8 26 , Rhodococcus qingshengii 7B 27 , Rhodococcus qingshengii VT6 28 , Priestia aryabhattai 25 29 , Gordonia amicalis 6-1 30 , Gordonia alkanivorans 135 31,32 , Gordonia polyisoprenivorans 135 33 , Rhodococcus opacus 1CP 34 , Rhodococcus opacus 3D 35 ).…”