High-Quality Whole-Genome Sequence of an Estradiol-Degrading Strain, Novosphingobium tardaugens NBRC 16725

Ibero, Juan; Sanz, David J.; Galán, Beatriz; Dı́az, Eduardo; Garcı́a, José Luis

doi:10.1128/mra.01715-18

Cited by 11 publications

(15 citation statements)

References 20 publications

(21 reference statements)

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“…In silico analysis of the assembled N. tardaugens genome (4,358,096 bp) [29] using as query the amino acid sequences of the coding genes responsible for TES degradation in C. testosteroni TA441 revealed the existence of a putative steroid degradation gene cluster covering a 26.4 kb region ( EGO55_13795 - EGO55_13670 (Figure 3). The predicted SD cluster is organized in two regions that are transcribed divergently, i.e., EGO55_13690 - EGO55_13670 and EGO55_13695 - EGO55_13795 (Figure 3b).…”

Section: Resultsmentioning

confidence: 99%

“…The recent reduction of the number of contigs in a previous work [29] allowed us to identify the genes that could be responsible for the degradation of C-19 steroids in N. tardaugens . A comparison with the genes described for other C-19 degradation pathways, particularly with those described for the degradation of TES in C. testosteroni , was carried out.…”

Section: Discussionmentioning

confidence: 99%

“…Molecular biology and DNA manipulations where performed as described elsewhere [31]. N. tardaugens genomic DNA was extracted as described before [29]. Plasmid DNA was purified using High Pure Plasmid Isolation Kit (Roche).…”

Section: Methodsmentioning

confidence: 99%

“…In this work, we have analysed the growth of N. tardaugens NBRC 16725 (strain ARI-1) with TES and other C-19 steroids as the sole carbon and energy sources. The complete genome sequence of this bacterium has been recently reported [29] allowing us to predict a SD gene cluster presumably involved in the catabolism of TES and other C-19 steroids. We have determined the expression of the catabolic genes by using a transcriptomic approach.…”

Section: Introductionmentioning

confidence: 99%

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Testosterone Degradative Pathway of Novosphingobium tardaugens

Ibero

Galán

Dı́az

et al. 2019

Genes

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In this work, we have shown that Novosphingobium tardaugens NBRC 16725 (strain ARI-1), a bacterial strain that was isolated due to its capacity to mineralize the estrogenic endocrine compound 17β-estradiol, is also able to mineralize testosterone, the androgenic endocrine compound. Using in silico analysis, we predicted a new putative steroid degradation (SD) gene cluster in strain ARI-1, which resembles genes involved in testosterone degradation in Comamonas testosteroni and other testosterone degrading bacteria like Actinobacteria (like Rhodococcus and Mycobacteria genera) although with significant differences in gene organization. A whole transcriptomic analysis of N. tardaugens revealed that testosterone produces a limited induction of the genes of the SD cluster that show a high basal expression in its absence. The 3β/17β-hydroxysteroid dehydrogenase involved in the first metabolic step of testosterone degradation was identified by using genetic and biochemical approaches. The construction of knockout mutant strains in the genes of the SD cluster together with in silico analyses suggests the existence of gene redundancy in the genome of N. tardaugens. This work will expand the knowledge about the metabolic pathways and biotransformation capabilities of a Gram-negative bacterium that could become a new model system in the bacterial steroid degradation field.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Testosterone Degradative Pathway of Novosphingobium tardaugens

Ibero

Galán

Dı́az

et al. 2019

Genes

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“…In this study, we used Novosphingobium tardaugens NBRC 16725 (formerly described as strain ARI-1), which was isolated in a sewage treatment plant in Tokyo (Japan) and is able to use sex hormones such as testosterone (TES), E2, E1, and E3 as sole carbon and energy sources (Fujii et al, 2002(Fujii et al, , 2003Ibero et al, 2019a). Recently, we have reported the complete sequence and assembly of this E2-degrading bacterium genome into a single contig (Ibero et al, 2019b). In this study, we have performed transcriptomic analysis that enabled the identification of the catabolic genes involved in estrogen degradation.…”

Section: Introductionmentioning

confidence: 99%

Unraveling the 17β-Estradiol Degradation Pathway in Novosphingobium tardaugens NBRC 16725

et al. 2020

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We have analyzed the catabolism of estrogens in Novosphingobium tardaugens NBRC 16725, which is able to use endocrine disruptors such as 17β-estradiol, estrone, and estriol as sole carbon and energy sources. A transcriptomic analysis enabled the identification of a cluster of catabolic genes (edc cluster) organized in two divergent operons that are involved in estrogen degradation. We have developed genetic tools for this estrogen-degrading bacterium, allowing us to delete by site-directed mutagenesis some of the genes of the edc cluster and complement them by using expression plasmids to better characterize their precise role in the estrogen catabolism. Based on these results, a catabolic pathway is proposed. The first enzyme of the pathway (17β-hydroxysteroid dehydrogenase) used to transform 17β-estradiol into estrone is encoded out of the cluster. A CYP450 encoded by the edcA gene performs the second metabolic step, i.e., the 4-hydroxylation of estrone in this strain. The edcB gene encodes a 4-hydroxyestrone-4,5-dioxygenase that opens ring A after 4-hydroxylation. The initial steps of the catabolism of estrogens and cholate proceed through different pathways. However, the degradation of estrogens converges with the degradation of testosterone in the final steps of the lower catabolic pathway used to degrade the common intermediate 3aα-H-4α(3′-propanoate)7a-β-methylhexahydro-1,5-indanedione (HIP). The TonB-dependent receptor protein EdcT appears to be involved in estrogen uptake, being the first time that this kind of proteins has been involved in steroid transport.

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