Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective <i>β</i>-Estradiol-Degrading Bacterium

Zhao, Hongyan; Tian, Kejian; Qiu, Qing; Wang, Yu; Zhang, Hongyan; Ma, Shuang; Jin, Shenbao; Huo, Hongliang

doi:10.1155/2018/3505428

Cited by 18 publications

(21 citation statements)

References 21 publications

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“…: WPAG00000000.1), which is also present in the genome of oestrogen-degrading Rhodococcus sp. strain DSSKP-R-001 (Zhao et al, 2018), but not in other Rhodococcus members incapable of degrading oestrogen. Moreover, the two homologous oestrogen-degrading gene clusters are both located on their megaplasmids (Fig.…”

Section: Identification Of the Oestrogen-degrading Genes Via Comparatmentioning

confidence: 90%

Mechanistic and phylogenetic insights into actinobacteria‐mediated oestrogen biodegradation in urban estuarine sediments

Hsiao

Chen

Meng

et al. 2021

Microbial Biotechnology

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Steroidal oestrogens are often accumulated in urban estuarine sediments worldwide at microgram per gram levels. These aromatic steroids have been classified as endocrine disruptors and group 1 carcinogens. Microbial degradation is a naturally occurring mechanism that mineralizes oestrogens in the biosphere; however, the corresponding genes in oestrogen-degrading actinobacteria remain unidentified. In this study, we identified a gene cluster encoding several putative oestrogen-degrading genes (aed; actinobacterial oestrogen degradation) in actinobacterium Rhodococcus sp. strain B50. Among them, the aedA and aedB genes involved in oestrogenic A-ring cleavage were identified through gene-disruption experiments. We demonstrated that actinobacterial oestrone 4-hydroxylase (AedA) is a cytochrome P450-type monooxygenase. We also detected the accumulation of two extracellular oestrogenic metabolites, including pyridinestrone acid (PEA) and 3aa-H-4a(3'-propanoate)-7ab-methylhexahydro-1,5-indanedione (HIP), in the oestrone-fed strain B50 cultures. Since actinobacterial aedB and proteobacterial edcB shared < 40% sequence identity, 4-hydroxyestrone 4,5-dioxygenase genes (namely aedB and edcB) could serve as a specific biomarker to differentiate the contribution of actinobacteria and proteobacteria in environmental oestrogen degradation. Therefore, 4-hydroxyestrone 4,5-dioxygenase genes and the extracellular metabolites PEA and HIP were used as biomarkers to investigate oestrogen biodegradation in an urban estuarine sediment. Interestingly, our data suggested that actinobacteria are active oestrogen degraders in the urban estuarine sediment.

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Section: Identification Of the Oestrogen-degrading Genes Via Comparatmentioning

confidence: 90%

Mechanistic and phylogenetic insights into actinobacteria‐mediated oestrogen biodegradation in urban estuarine sediments

Hsiao

Chen

Meng

et al. 2021

Microbial Biotechnology

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“…For example, Rhodococcus equi Y50156 and Rhodococcus zopfii Y50158 have a degradation rate > 95 % at 24 h for 100 mg/L concentrations of the four estrogens listed above [11], and Rhodococcus rubber KC4 has a 99% degradation rate at 24 h for E2a at a concentration of 3 mg/L [15]. In our previous study, the degradation rate at 72 h for 50 mg/L E2 by R. equi DSSKP-R-001 was 97% [35], and the degradation rates at 96 h of 30 mg/L E1, E2, and EE2 were 100%, 100%, and 90%, respectively. Therefore, the Rhodococcus.…”

Section: Introductionmentioning

confidence: 88%

The Analysis of Estrogen-Degrading and Functional Metabolism Genes in Rhodococcus equi DSSKP-R-001

Tian

Meng

et al. 2020

International Journal of Genomics

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Estrogen contamination is recognized as one of the most serious environmental problems, causing widespread concern worldwide. Environmental estrogens are mainly derived from human and vertebrate excretion, drugs, and agricultural activities. The use of microorganisms is currently the most economical and effective method for biodegradation of environmental estrogens. Rhodococcus equi DSSKP-R-001 (R-001) has strong estrogen-degrading capabilities. Our study indicated that R-001 can use different types of estrogen as its sole carbon source for growth and metabolism, with final degradation rates above 90%. Transcriptome analysis showed that 720 (E1), 983 (E2), and 845 (EE2) genes were significantly upregulated in the estrogen-treated group compared with the control group, and 270 differentially expressed genes (DEGs) were upregulated across all treatment groups. These DEGs included ABC transporters; estrogen-degrading genes, including those that perform initial oxidation and dehydrogenation reactions and those that further degrade the resulting substrates into small molecules; and metabolism genes that complete the intracellular transformation and utilization of estrogen metabolites through biological processes such as amino acid metabolism, lipid metabolism, carbohydrate metabolism, and the tricarboxylic acid cycle. In summary, the biodegradation of estrogens is coordinated by a metabolic network of estrogen-degrading enzymes, transporters, metabolic enzymes, and other coenzymes. In this study, the metabolic mechanisms by which Rhodococcus equi R-001 degrades various estrogens were analyzed for the first time. A new pollutant metabolism system is outlined, providing a starting point for the construction of engineered estrogen-degrading bacteria.

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“…Zhao and co-workers state that Rhodococcus strain sp. DSSKP-R-001, interesting for its beta-estradiol-degrading potential, contains 8 CRISPRs [144]. However, the authors do not state how these were identified.…”

Section: Discussionmentioning

confidence: 99%

The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870

Frederick

Hennessy

Horn³

et al. 2020

BMC Genomics

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BackgroundRhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst.ResultsThe genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase.Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci.ConclusionsThe sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.

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Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium

Cited by 18 publications

References 21 publications

Mechanistic and phylogenetic insights into actinobacteria‐mediated oestrogen biodegradation in urban estuarine sediments

Mechanistic and phylogenetic insights into actinobacteria‐mediated oestrogen biodegradation in urban estuarine sediments

The Analysis of Estrogen-Degrading and Functional Metabolism Genes in Rhodococcus equi DSSKP-R-001

The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870

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