Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jul 1:12:670928.
doi: 10.3389/fmicb.2021.670928. eCollection 2021.

Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557

Sarah L Harthern-Flint  1 , Jan Dolfing  1   2 , Wojciech Mrozik  1   3 , Paola Meynet  1 , Lucy E Eland  4 , Martin Sim  4 , Russell J Davenport  1
Affiliations

Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557

Sarah L Harthern-Flint et al. Front Microbiol. .

Abstract

Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.

Keywords: Rhodococcus equi; bacteria; degradation; genes; genome; oestrogen.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
The average growth of R. equi ATCC13557 (A) whilst being grown in the different conditions, exposed to mixed oestrogens E1, E2, and EE2 and E2 only. Comparison of the average growth of R. equi ATCC13557 without oestrogen (control), exposed to mixed oestrogens E2 and EE2, E2-only, and abiotic. The average concentrations of oestrogens were measured over time, in mixed conditions E2 and EE2 (B), and in E2-only condition (C). The error bars represent standard deviation.
FIGURE 2
FIGURE 2
The CCT (Grant et al., 2012) genome map comparing R. equi ATCC 13557 to the R. equi 103S reference genome (A). Starting from the outermost ring the feature rings depict; 1. COG features of the forward strand sequence; 2. forward strand sequence features of R. equi ATTC 13557; 3. reverse strand sequence features of R. equi ATCC 13557; 4. the COG features of the reverse strand sequence; 5. the sequence similarity was detected by BLAST comparisons conducted between nucleotide sequences from R. equi ATCC 13557 and R. equi 103S; and the final rings display the GC content and the GC skew. A gene cluster encoding enzymes potentially involved in oestrogen degradation is labelled on the outermost ring. A RAST diagram of a chromosomal region around the focus gene coding for 3-carboxyethylcatechol 2,3-dioxygenase “JO861_14995” (red, 1) (B). The other genes present code for 2-hydroxymuconic semialdehyde hydrolase “JO861_15000” (light green, 2), 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase “JO861_15020” (yellow, 5), 3-(3-hydroxy-phenyl) propionate hydroxylase “JO861_15005” (turquoise, 6), 3-oxosteroid 1-dehydrogenase “JO861_15025” (dark green, 8), and transcriptional regulator IcIR family (blue, 10). The grey arrows are genes with the relative position conserved found in at least four other species.
FIGURE 3
FIGURE 3
The subsystem distribution, coverage, and counts within the SPAdes assembly of R. equi ATCC13557 as annotated by Rapid Annotation System Technology (RAST) server (Aziz et al., 2008; Overbeek et al., 2014; Brettin et al., 2015).
FIGURE 4
FIGURE 4
A phylogenetic tree of R. equi ATCC13557 and genomes with the closest genomic identities which were generated by T-REX and visualised in iTOL version 6.1.1, based on ANI analyses (Boc et al., 2012; Richter et al., 2016; Letunic and Bork, 2019).
FIGURE 5
FIGURE 5
Synteny plots showing the BLAST hits of gene sequences in a database of potential oestrogen degradation genes, mapped to the contigs of; Sphingomonas strain KC8, Pseudomonas putida SJTE-1, and R. equi ATCC13557. The diagram of R. equi ATCC13557 shows the two highest-scoring BLAST sequences encoding 3-ketosteroid 1-oxosteroid dehydrogenase. The different coloured arrows represent the different sequences, with the sequence accession denoted below, encoding enzymes denoted above each arrow.
FIGURE 6
FIGURE 6
Plots produced by M1CR0B1AL1Z3R (Avram et al., 2019) showing the ORF count per genome (A), and orthologous groups shared between the genomes of oestrogen degrading bacteria (B).
FIGURE 7
FIGURE 7
Phylogenetic trees showing the evolutionary relationship, in the orthologous genes encoding 17β-hydroxysteroid dehydrogenase (A), cytochrome P450 monooxygenase (B), and extradiol dioxygenase (C). The nucleic acid sequences from actinobacteria are shown in black, proteobacteria are shown in red, and non-oestrogen degrading bacterial genomes of genes encoding (i) P450 monooxygenase (BisdB), (ii) 3-ketosteroid-delta-1-dehydrogenase (kstD and TesH), (iii) 3-ketosteroid-Δ4(5α)-dehydrogenase (TesI), and (iv) dioxygenase (HsaC), which function in bisphenol A, cholate, testosterone, and cholesterol degradation, respectively, are shown in blue.
FIGURE 8
FIGURE 8
Plots produced by M1CR0B1AL1Z3R (Avram et al., 2019) showing the ORF count per genome (A), and orthologous groups shared between the genomes of cholesterol degrading bacteria (B).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Adeel M., Song X., Wang Y., Francis D., Yang Y. (2017). Environmental impact of estrogens on human, animal and plant life: a critical review. Environ. Int. 99 107–119. 10.1016/j.envint.2016.12.010 - DOI - PubMed
    1. Afgan E., Baker D., van den Beek M., Blankenberg D., Bouvier D., Čech M., et al. (2016). The Galaxy platform for accessible, reproducible, and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44 W3–W10. 10.1093/nar/gkw343 - DOI - PMC - PubMed
    1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402. 10.1093/nar/25.17.3389 - DOI - PMC - PubMed
    1. Andaluri G., Suri R. P. S., Kumar K. (2012). Occurrence of estrogen hormones in biosolids, animal manure and mushroom compost. Environ. Monit. Assess. 184 1197–1205. 10.1007/s10661-011-2032-8 - DOI - PubMed
    1. Aris A. Z., Shamsuddin A. S., Praveena S. M. (2014). Occurrence of 17α-ethynylestradiol (EE2) in the environment and effect on exposed biota: a review. Environ. Int. 69 104–119. 10.1016/j.envint.2014.04.011 - DOI - PubMed

LinkOut - more resources