Characterization and genomic analysis of Gordonia alkanivorans 135, a promising dibenzothiophene-degrading strain

Delegan, Yanina; Kocharovskaya, Yulia; Frantsuzova, Ekaterina; Streletskii, Rostislav; Vetrova, Anna

doi:10.1016/j.btre.2021.e00591

Cited by 12 publications

(19 citation statements)

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“…In the annotated genomes of G. amicalis strains 6-1 and 1D, the presence of this enzyme can be inferred for both strains ( Figure S5a ). In spite of phenomenological observations on growth of G. alkanivorans strain 135 on n -alkanes, oil, and diesel fuel [ 39 ], it contained no monooxygenase enzymes (EC 1.14.15.3) ( Figure S5b ). These data support the conclusion that alkane-degrading properties of strain 135 result from the presence of CYP153 family alkane hydroxylases.…”

Section: Resultsmentioning

confidence: 92%

“…Using NCBI PGAP pipeline, in the chromosome 6-1 were predicted 4739 genes, including 4429 protein-coding genes, 9 rRNAs, 47 tRNAs and 3 non-coding RNAs. Table 1 presents the general characteristics of genomes of the strain G. amicalis 6-1 and previously described strains G. amicalis 1D [ 37 ] and G. alkanivorans 135 [ 38 , 39 ], utilizing DBT as the sulfur source. Maps of circular chromosomes of strains 1D and 135 and plasmid pG135 are given in Figure S2 .…”

Section: Resultsmentioning

confidence: 99%

“…The genomes of two bacterial strains, Gordonia amicalis 1D and Gordonia alkanivorans 135 (VKM Ac-2849D), utilizing DBT as the sole sulfur source, were sequenced and described previously [ 37 , 38 , 39 ]. The genome of strain 1D is available from GenBank/EMBL/DDBJ under accession number GCA_002327125.1.…”

Section: Methodsmentioning

confidence: 99%

“…We have previously isolated two Gordonia strains, Gordonia amicalis 1D and Gordonia alkanivorans 135, which utilize DBT as the sole sulfur source for growth [ 37 , 38 , 39 ]. Genome sequencing showed that these strains had no dsz operon, required for the 4S pathway of thiophene desulfurization.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…. In this process, they oxidize sul des into sulfates and release them into the environment, which helps reduce or eliminate sul de waste emissions, thereby mitigating environmental pollution (Feng et al 2016;Delegan et al 2021). Consequently, bacteria belonging to the Gordonia genus are considered promising resources for biodesulfurization.…”

Section: Isolation and Identi Cation Of Strain Swx-4mentioning

confidence: 99%

Genetic and comparative genome analysis of the dibenzothiophene-desulfurizing Gordonia SWX-4

Xu,

Cheng,

et al. 2023

Preprint

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Biodesulfurization of crude oil is a highly promising technology for achieving thorough desulfurization. In this study, a bacterial strain, designated as SWX-4, was isolated from sandstone oil in the Ordos Basin that had the ability to utilize dibenzothiophene (DBT) as a carbon source. Through physiological and biochemical characterization as well as 16S rRNA sequencing, the isolate was identified as Gordonia sp. The genome of strain SWX-4 was found to be 5,303,410 bp in size, with a GC content of 67.44%. It comprised 12 rRNA genes, 51 tRNA genes, and two plasmids. Genome analysis revealed the presence of 4,683 functional genes potentially involved in DBT desulfurization, as well as the oxidation of alkanes and aromatic compounds. Notably, the genome of strain SWX-4 also contained genes encoding sfnG, sfnB, and terD, which are known to be responsible for the desulfurization activity of DBT. These genes exhibited functional similarity to the well-conserved dszABC operons. Furthermore, a comparative genomic analysis of 43 Gordonia strains isolated from various habitats was conducted to explore their genetic diversity. The results revealed that Gordonia sp. possesses an open pan-genome with a total of 774 core genes present across all strains. On average, these core genes accounted for 18% of each individual genome. Additionally, phylogenetic tree analysis and the distribution of accessory genes showed that each strain harbored a distinct set of unique genes. Interestingly, genes associated with biodesulfurization were found to be distributed among different branches of the phylogenetic tree. This suggests that these strains have the capacity to acquire new genes through horizontal gene transfer from their environments, thereby increasing the diversity of their bacterial genomes. However, we did not observe a direct evolutionary correlation between the bacterial genome and desulfurization metabolism. Overall, our findings provide valuable insights into the biodegradation of DBT by the SWX-4 strain and offer an efficient bacterial resource for biodesulfurization.

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Surface-Enhanced Raman Spectroscopy (SERS) for the Characterization of Biodesulfurization of Gordonia HS-126-4N by 4,6-Dimethyl Dibenzothiophene

Ghaffar,

E Habiba,

Majeed

et al. 2023

Analytical Letters

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Characterization and genomic analysis of Gordonia alkanivorans 135, a promising dibenzothiophene-degrading strain

Cited by 12 publications

References 28 publications

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

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

Genetic and comparative genome analysis of the dibenzothiophene-desulfurizing Gordonia SWX-4

Surface-Enhanced Raman Spectroscopy (SERS) for the Characterization of Biodesulfurization of Gordonia HS-126-4N by 4,6-Dimethyl Dibenzothiophene

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