Identification and genome analysis of Deinococcus actinosclerus SJTR1, a novel 17β-estradiol degradation bacterium

Abstract

Biodegradation with microorganisms is considered as an efficient strategy to remove the environmental pollutants. In this work, Deinococcus actinosclerus SJTR1 isolated from the wastewater was confirmed with great degradation capability to 17β-estradiol, one typical estrogen chemical. It could degrade nearly 90% of 17β-estradiol (10 mg/L) in 5 days and transform it into estrone; its degradation kinetics fitted for the first-order kinetic equation. The whole genome sequence of D. actinosclerus SJTR1 was obtained and annotated, containing one chromosome (3,315,586 bp) and four plasmids (ranging from 17,267 bp to 460,244 bp). A total of 3913 CDSs and 73 RNA genes (including 12 rRNA genes, 50 tRNA genes, and 11 ncRNA genes) were identified in its whole genome sequence. On this basis, a series of potential genes involved in steroid metabolism and stress responses of D. actinosclerus SJTR1 were predicted. It is the first report of Deinococcus strain with the degradation capability to estrogens. This work could enrich the genome sources of the estrogen-degrading strains and promote the degradation mechanism study of 17β-estradiol in bacteria.

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

“…ES2-1 was expressed in the presence of E2 (Whirl-Carrillo et al, 2012;Hsiao et al, 2020;Ibero et al, 2020;Li et al, 2021). However, gene expression or gene knockout experiments are required to provide conclusive Hu et al, 2011;Liang et al, 2012;Zhang Y. et al, 2012;Ye et al, 2017;Xiong et al, 2018Xiong et al, , 2020Zhao et al, 2018;Qiu et al, 2019;Ibero et al, 2020;Pratush et al, 2020;Tian et al, 2020; Zhao et al, 2018;Hsiao et al, 2020;Ibero et al, 2020;Tian et al, 2020;Xiong et al, 2020;Li et al, 2021 evidence that these genes are responsible for the metabolism of E2 by R. equi ATCC13557.…”

“…More recent studies have confirmed both the existence of orthologues for the above clusters and the genes on them, in addition to their function (through gene knock-out experiments) or upregulation in transcriptomic studies. Thus, orthologues of 17β-hydroxysteroid dehydrogenase ( oecA ), which encodes an enzyme that transforms E2 to E1, have been identified in N. tardaugens NBRC16725 ( Ibero et al, 2020 ), Deinococcus actinosclerus SJTR1 ( Xiong et al, 2018 ), and the actinobacteria, Rhodococcus sp. strain DSSKP-R-001 ( Zhao et al, 2018 ; Tian et al, 2020 ) and Rhodococcus sp.…”

“…DSSKY-A-001, Novosphingobium sp. ES2-1, and L. sphaericus DH-B01, the first step in the degradation of E2 appears to be the oxidation of the C-17 hydroxyl position by an SDR such as 17β-hydroxysteroid dehydrogenase to produce E1 ( Hu et al, 2011 ; Qin et al, 2016 ; Zheng et al, 2016 ; Chen et al, 2017 ; Ye et al, 2017 ; Xiong et al, 2018 , 2020 ; Qiu et al, 2019 ; Wang et al, 2019 ; Wu et al, 2019 ; Wang Y. et al, 2020 ; Li et al, 2021 ). However, there are examples of different E2 degradation pathways reported in bacteria, such as hydroxylation at different positions within different saturated rings (B, C, or D) to produce 4-hydroxyestradiol (4-OH-E2), keto-E1, keto-E2, or E3 ( Xuan et al, 2008 ; Kurisu et al, 2010 ; Yu et al, 2013 ).…”

Suitability of Immobilized Systems for Microbiological Degradation of Endocrine Disrupting Compounds

“…Bacteria that degrade these hormones belong to genera such as Bacillus , Virgibacillus , Novosphingobium , Rhodococcus , Acinetobacter , Pseudomonas , Sphingomonas , Enterobacter , Klebsiella , Aeromonas , Comamonas , Thauera , Deinococcus , Stenotrophomonas and cyanobacteria [ 3 , 4 , 6 , 7 , 10 , 12 , 25 , 28 , 31 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. Raphidocelis subcapitata , Chlorella vulgaris , Chlorococcus and Scenedesmus quadricauda belong to algae capable of removing hormones [ 11 , 26 , 40 , 41 ].…”

“…This reaction is of great environmental significance as this reduces the total estrogenic activity due to the oxygenation of the phenol group of 17β-estradiol to ketone moiety [ 6 , 10 , 22 , 35 , 38 ]. Xiong et al [ 38 ], during genome analysis of Deinococcus actinosclerus SJTR1, found 18 genes encoding short-chain dehydrogenase/reductase (SDR), probably engaged in transformation 17β-estradiol to estrone. Estrone can be degraded in various pathways, during estrone metabolism by Rhodococcus hoagii BH2–1.…”