Identification of novel catabolic genes involved in 17β-estradiol degradation by Novosphingobium sp. ES2-1

Conversion of estriol to estrone: A bacterial strategy for the catabolism of estriol

Natural estrogens, including estrone (E1), 17β-estradiol (E2), and estriol (E3), are potentially carcinogenic pollutants commonly found in water and soil environments. Bacterial metabolic pathway of E2 has been studied; however, the catabolic products of E3 have not been discovered thus far. In this study, Novosphingobium sp. ES2-1 was used as the target strain to investigate its catabolic pathway of E3. The metabolites of E3 were identified by high performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS) combined with stable 13C3-labeling. Strain ES2-1 could almost completely degrade 20 mg∙L-1 of E3 within 72 h under the optimal conditions of 30°C and pH 7.0. When inoculated with strain ES2-1, E3 was initially converted to E1 and then to 4-hydroxyestrone (4-OH-E1), which was then cleaved to HIP (metabolite A6) via the 4, 5-seco pathway or cleaved to the B loop via the 9,10-seco pathway to produce metabolite with a long-chain ketone structure (metabolite B4). Although the ring-opening sequence of the above two metabolic pathways was different, the metabolism of E3 was achieved especially through continuous oxidation reactions. This study reveals that, E3 could be firstly converted to E1 and then to 4-OH-E1, and finally degraded into small molecule metabolites through two alternative pathways, thereby reducing E3 pollution in water and soil environments.

Functional analysis, diversity, and distribution of the ean cluster responsible for 17β-estradiol degradation in sphingomonads

17β-estradiol (E2) is a natural endocrine disruptor that is frequently detected in surface and groundwater sources, thereby threatening ecosystems and human health. The newly isolated E2-degrading strain Sphingomonas colocasiae C3-2 can degrade E2 through both the 4,5-seco pathway and the 9,10-seco pathway; the former is the primary pathway supporting the growth of this strain and the latter is a branching pathway. The novel gene cluster ean was found to be responsible for E2 degradation through the 4,5-seco pathway, where E2 is converted to estrone (E1) by EanA, which belongs to the short-chain dehydrogenases/reductases (SDR) superfamily. A three-component oxygenase system (including the P450 monooxygenase EanB1, the small iron-sulfur protein ferredoxin EanB2, and the ferredoxin reductase EanB3) was responsible for hydroxylating E1 to 4-hydroxyestrone (4-OH-E1). The enzymatic assay showed that the proportion of the three components is critical for its function. The dioxygenase EanC catalyzes ring A cleavage of 4-OH-E1, and the oxidoreductase EanD is responsible for the decarboxylation of the ring A-cleavage product of 4-OH-E1. EanR, a TetR family transcriptional regulator, acts as a transcriptional repressor of the ean cluster. The ean cluster was also found in other reported E2-degrading sphingomonads. In addition, the novel two-component monooxygenase EanE1E2 can open ring B of 4-OH-E1 via the 9,10-seco pathway, but its encoding genes are not located within the ean cluster. These results refine research on genes involved in E2 degradation and enrich the understanding of the cleavages of ring A and ring B of E2.IMPORTANCESteroid estrogens have been detected in diverse environments, ranging from oceans and rivers to soils and groundwater, posing serious risks to both human health and ecological safety. The United States National Toxicology Program and the World Health Organization have both classified estrogens as Group 1 carcinogens. Several model organisms (proteobacteria) have established the 4,5-seco pathway for estrogen degradation. In this study, the newly isolated Sphingomonas colocasiae C3-2 could degrade E2 through both the 4,5-seco pathway and the 9,10-seco pathway. The novel gene cluster ean (including eanA, eanB1, eanC, and eanD) responsible for E2 degradation by the 4,5-seco pathway was identified; the novel two-component monooxygenase EanE1E2 can open ring B of 4-OH-E1 through the 9,10-seco pathway. The TetR family transcriptional regulator EanR acts as a transcriptional repressor of the ean cluster. The cluster ean was also found to be present in other reported E2-degrading sphingomonads, indicating the ubiquity of the E2 metabolism in the environment.

Adaptive responses and metabolic strategies of Novosphingobium sp. ES2-1-17β-estradiol analyzed through integration of genomic and proteomic approaches

Environmental 17β-estradiol (E2) can cause potential harm to ecological balance and human health. Novosphingobium sp. ES2-1 is an E2-degrading bacterium previously obtained, which converts E2 to estrone (E1) and then to 4-hydroxyestrone (4-OH-E1) followed by oxidation to form metabolites with long-chain structure during upstream degradation. Herein, we found that intracellular enzymes were the major contributors to E2 biodegradation by strain ES2-1. A total of 243 proteins were dys-expressed under E2 condition, 123 were up-regulated and 120 were down-regulated thereinto. The up-regulated members of ABC transport systems, aromatics degradation, and fatty acid degradation indicated a reinforced transfer and utilization of E2. Cytochrome P450 monooxygenase (EstP1), 2-keto-4-pentenoate hydratase, pyruvate dehydrogenase, acetyl-CoA acetyltransferase, TonB-dependent receptor were involved in E2 catabolism. During downstream degradation, the metabolites with long-chain structure were decomposed adopting β-oxidation pattern and ultimately entered the TCA cycle; 2-keto-4-pentenoic acid might be an emblematic product of such process. Furthermore, E2 converting to E1 was catalyzed by 17β-dehydrogenase probably encoded by IM701_16645 or IM701_16910; 4-OH-E1 meta-cleavage was catalyzed by a dioxygenase encoded by IM701_20340 or IM701_21000 or IM701_09625. Our study provided an in-depth insight into the adaptive responses and metabolic strategies of Novosphingobium to E2.

Characterization and low-temperature biodegradation mechanism of 17β-estradiol-degrading bacterial strain Rhodococcus sp. RCBS9

Steroidal estrogens residues in the environment can be a serious hazard to humans and animals and has been listed as group 1 carcinogens by World Health Organization (WHO). Microbial degradation is one of the effective strategies for the removal of such contaminants. In this study, a low-temperature degrading bacterial strain (Rhodococcus sp. RCBS9) was isolated from the soil of a dairy farm for 17β-estradiol (E2) degradation. The strain RCBS9 exhibited an efficient degradation potential at low temperatures. To lean how different factors influence E2 degradation, we have found a major role of intracellular enzymes in E2 degradation. Genomic and metabolomic analyses have suggested potential degradation genes and four metabolic pathways. These findings provide valuable strain resources for the low temperature bioremediation of E2 contamination and insights into E2 biodegradation mechanism.

A Novel Estrone Degradation Gene Cluster and Catabolic Mechanism in Microbacterium oxydans ML-6

Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.

Efficient heterologous expression of cytochrome P450 enzymes in microorganisms for the biosynthesis of natural products

Natural products, a chemically and structurally diverse class of molecules, possess a wide spectrum of biological activities, have been used therapeutically for millennia, and have provided many lead compounds for the development of synthetic drugs. Cytochrome P450 enzymes (P450s, CYP) are widespread in nature and are involved in the biosynthesis of many natural products. P450s are heme-containing enzymes that use molecular oxygen and the hydride donor NAD(P)H (coupled via enzymic redox partners) to catalyze the insertion of oxygen into C-H bonds in a regio- and stereo-selective manner, effecting hydroxylation and several other reactions. With the rapid development of systems biology, numerous novel P450s have been identified for the biosynthesis of natural products, but there are still several challenges to the efficient heterologous expression of active P450s. This review covers recent developments in P450 research and development, including the properties and functions of P450s, discovery and mining of novel P450s, modification and screening of P450 mutants, improved heterologous expression of P450s in microbial hosts, efficient whole-cell transformation with P450s, and current applications of P450s for the biosynthesis of natural products. This resource provides a solid foundation for the application of highly active and stable P450s in microbial cell factories to biosynthesize natural products.

Whole-Cell P450 Biocatalysis Using Engineered Escherichia coli with Fine-Tuned Heme Biosynthesis

By exploiting versatile P450 enzymes, whole-cell biocatalysis can be performed to synthesize valuable compounds in Escherichia coli. However, the insufficient supply of heme limits the whole-cell P450 biocatalytic activity. Here a strategy for improving intracellular heme biosynthesis to enhance the catalytic efficiencies of P450s is reported. After comparing the effects of improving heme transport and biosynthesis on P450 activities, intracellular heme biosynthesis is optimized through the integrated expression of necessary synthetic genes at proper ratios and the assembly of rate-limiting enzymes using DNA-guided scaffolds. The intracellular heme level is fine-tuned by the combined use of mutated heme-sensitive biosensors and small regulatory RNA systems. The catalytic efficiencies of three different P450s, BM3, sca-2, and CYP105D7, are enhanced through fine-tuning heme biosynthesis for the synthesis of hydroquinone, pravastatin, and 7,3',4'-trihydroxyisoflavone as example products of chemical intermediate, drug, and natural product, respectively. This strategy of fine-tuned heme biosynthesis will be generally useful for developing whole-cell biocatalysts involving hemoproteins.

Bioconversion of 4-hydroxyestradiol by extradiol ring-cleavage dioxygenases from Novosphingobium sp. PP1Y

Livestock breeding activities and pharmaceutical wastes lead to considerable accumulation of steroid hormones and estrogens in wastewaters. Here estrogens act as pro-cancerogenic agents and endocrine disruptors interfering with the sexual development of aquatic animals and having toxic effects in humans. Environmental bacteria play a vital role in estrogens degradation. Their wide reservoir of enzymes, such as ring cleavage dioxygenases (RCDs), can degrade the steroid nucleus, catalyzing the meta-cleavage of A, B or D steroid rings. In this work, 4 extra-diol ring cleavage dioxygenases (ERCDs), PP28735, PP26077, PP00124 and PP00193, were isolated from the marine sphingomonad Novosphingobium sp. PP1Y and characterized. Enzymes kinetic parameters were determined on different synthetic catecholic substrates. Then, the bioconversion of catechol estrogens was evaluated. PP00124 showed to be an efficient catalyst for the degradation of 4-hydroxyestradiol (4-OHE2), a carcinogenic hydroxylated derivate of E2. 4-OHE2 complete cleavage was obtained using PP00124 both in soluble form and in whole recombinant E. coli cells. LC-MS/MS analyses confirmed the generation of a semialdehyde product, through A-ring meta cleavage. To the best of our knowledge, PP00124 is the first characterized enzyme able to directly degrade 4-OHE2 via meta cleavage. Moreover, the complete 4-OHE2 biodegradation using recombinant whole cells highlighted advantages for bioremediation purposes.

Transcriptome profiling of Microbacterium resistens MZT7 reveals mechanisms of 17β-estradiol response and biotransformation

17β-estradiol (E2) pollution has attracted much attention, and the existence of E2 poses certain risks to the environment and human health. However, the mechanism of microbial degradation of E2 remains unclear. In this study, the location of E2-degrading enzymes was investigated, and transcriptome analysis of Microbacterium resistens MZT7 (M. resistens MZT7) exposed to E2. The degradation of E2 by M. resistens MZT7 was via the biological action of E2-induced intracellular enzymes. With the RNA sequencing, we found 1109 differentially expressed genes (DEGs). Among them, 773 genes were up-regulated and 336 genes were down-regulated. The results of the RNA sequencing indicated the DEGs were related to transport, metabolism, and stress response. Genes for transport, transmembrane transport, oxidoreductase activity, ATPase activity, transporter activity and quorum sensing were up-regulated. Genes for the tricarboxylic acid cycle, ribosome, oxidative phosphorylation and carbon metabolism were down-regulated. In addition, heterologous expression of one enzymes efficiently degraded E2. These findings provide some new insights into the molecular mechanism of biotransformation of E2 by M. resistens MZT7.

Characterization and Degradation Pathways of Microbacterium resistens MZT7, A Novel 17β-Estradiol-Degrading Bacterium

Due to the ecotoxicity of 17β-estradiol (E2), residual E2 in the environment poses potential risks to human and animal health and ecosystems. Biodegradation is considered one of the most effective strategies to remove E2 from the environment. Here, a novel, efficient E2-degrading bacterial strain Microbacterium resistens MZT7 was isolated from activated sludge and characterized. The genome of strain MZT7 contained 4,011,347 bp nucleotides with 71.26% G + C content and 3785 coding genes. There was 86.7% transformation efficiency of 10 mg/L E2 by strain MZT7 after incubation for 5 d at optimal temperature (30 °C) and pH (7.0). This strain was highly tolerant to ranges in pH (5.0-11.0), temperature (20-40 °C), and salinity (2-8%). Adding sources of carbon (glucose, maltose, sucrose, or lactose) or nitrogen sources (urea, peptone, or beef extract) promoted the degradation of E2 by strain MZT7. However, when yeast extract was added as a nitrogen source, the degradation efficiency of E2 was inhibited. Metabolites were analyzed by LC-MS and three metabolic pathways of E2 degradation were proposed. Further, the intermediates dehydroepiandrosterone and androsta-1,4-diene-3,17-dione were detected, as well as identification of kshB and fadD3 genes by KEGG, confirming one E2 degradation pathway. This study provided some insights into E2 biodegradation.

Identification of essential β-oxidation genes and corresponding metabolites for oestrogen degradation by actinobacteria

Steroidal oestrogens (C₁₈) are contaminants receiving increasing attention due to their endocrine‐disrupting activities at sub‐nanomolar concentrations. Although oestrogens can be eliminated through photodegradation, microbial function is critical for removing oestrogens from ecosystems devoid of sunlight exposure including activated sludge, soils and aquatic sediments. Actinobacteria were found to be key oestrogen degraders in manure‐contaminated soils and estuarine sediments. Previously, we used the actinobacterium Rhodococcus sp. strain B50 as a model microorganism to identify two oxygenase genes, aedA and aedB, involved in the activation and subsequent cleavage of the estrogenic A‐ring respectively. However, genes responsible for the downstream degradation of oestrogen A/B‐rings remained completely unknown. In this study, we employed tiered comparative transcriptomics, gene disruption experiments and mass spectrometry‐based metabolite profile analysis to identify oestrogen catabolic genes. We observed the up‐regulation of thiolase‐encoding aedF and aedK in the transcriptome of strain B50 grown with oestrone. Consistently, two downstream oestrogenic metabolites, 5‐oxo‐4‐norestrogenic acid (C₁₇) and 2,3,4‐trinorestrogenic acid (C₁₅), were accumulated in aedF‐ and aedK‐disrupted strain B50 cultures. Disruption of fadD3 [3aα‐H‐4α(3'‐propanoate)‐7aβ‐methylhexahydro‐1,5‐indanedione (HIP)‐coenzyme A‐ligase gene] in strain B50 resulted in apparent HIP accumulation in oestrone‐fed cultures, indicating the essential role of fadD3 in actinobacterial oestrogen degradation. In addition, we detected a unique meta‐cleavage product, 4,5‐seco‐estrogenic acid (C₁₈), during actinobacterial oestrogen degradation. Differentiating the oestrogenic metabolite profile and degradation genes of actinobacteria and proteobacteria enables the cost‐effective and time‐saving identification of potential oestrogen degraders in various ecosystems through liquid chromatography–mass spectrometry analysis and polymerase chain reaction‐based functional assays.

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

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.