Identification of a novel steroid inducible gene associated with the beta hsd locus of Comamonas testosteroni

Comprehensive summary of steroid metabolism in Comamonas testosteroni TA441: entire degradation process of basic four rings and removal of C12 hydroxyl group

Comamonas testosteroni is one of the representative aerobic steroid-degrading bacteria. We previously revealed the mechanism of steroidal A,B,C,D-ring degradation by C. testosteroni TA441. The corresponding genes are located in two clusters at both ends of a mega-cluster of steroid degradation genes. ORF7 and ORF6 are the only two genes in these clusters, whose function has not been determined. Here, we characterized ORF7 as encoding the dehydrase responsible for converting the C12β hydroxyl group to the C10(12) double bond on the C-ring (SteC), and ORF6 as encoding the hydrogenase responsible for converting the C10(12) double bond to a single bond (SteD). SteA and SteB, encoded just upstream of SteC and SteD, are in charge of oxidizing the C12α hydroxyl group to a ketone group and of reducing the latter to the C12β hydroxyl group, respectively. Therefore, the C12α hydroxyl group in steroids is removed with SteABCD via the C12 ketone and C12β hydroxyl groups. Given the functional characterization of ORF6 and ORF7, we disclose the entire pathway of steroidal A,B,C,D-ring breakdown by C. testosteroni TA441.IMPORTANCEStudies on bacterial steroid degradation were initiated more than 50 years ago, primarily to obtain materials for steroid drugs. Now, their implications for the environment and humans, especially in relation to the infection and the brain-gut-microbiota axis, are attracting increasing attention. Comamonas testosteroni TA441 is the leading model of bacterial aerobic steroid degradation with the ability to break down cholic acid, the main component of bile acids. Bile acids are known for their variety of physiological activities according to their substituent group(s). In this study, we identified and functionally characterized the genes for the removal of C12 hydroxyl groups and provided a comprehensive summary of the entire A,B,C,D-ring degradation pathway by C. testosteroni TA441 as the representable bacterial aerobic degradation process of the steroid core structure.

Identification of "missing links" in C- and D-ring cleavage of steroids by Comamonas testosteroni TA441

Comamonas testosteroni TA441 is capable of aerobically degrading steroids through the aromatization and cleavage of the A- and B-rings, followed by D- and C-ring cleavage via β-oxidation. While most of the degradation steps have been previously characterized, a few intermediate compounds remained unidentified. In this study, we proposed that the cleavage of the D-ring at C13-17 required the ScdY hydratase, followed by C-ring cleavage via the ScdL1L2 transferase. The anticipated reaction was expected to yield 6-methyl-3,7-dioxo-decane-1,10-dioic acid-coenzyme A (CoA) ester. To confirm this hypothesis, we constructed a plasmid enabling the induction of targeted genes in TA441 mutant strains. Induction experiments of ScdL1L2 revealed that the major product was 3-hydroxy-6-methyl-7-oxo-decane-1,10-dioic acid-CoA ester. Similarly, induction experiments of ScdY demonstrated that the substrate of ScdY was a geminal diol, 17-dihydroxy-9-oxo-1,2,3,4,5,6,10,19-octanorandrost-8(14)-en-7-oic acid-CoA ester. These findings suggest that ScdY catalyzes the addition of a water molecule at C14 of 17-dihydroxy-9-oxo-1,2,3,4,5,6,10,19-octanorandrost-8(14)-en-7-oic acid-CoA ester, leading to D-ring cleavage at C13-17. Subsequently, the C9 ketone of the D-ring cleavage product is converted to a hydroxyl group, followed by C-ring cleavage, resulting in the production of 3-hydroxy-6-methyl-7-oxo-decane-1,10-dioic acid-CoA ester.IMPORTANCEStudies on bacterial steroid degradation were initiated more than 50 years ago primarily to obtain substrates for steroid drugs. In recent years, the role of steroid-degrading bacteria in relation to human health has gained significant attention, as emerging evidence suggests that the intestinal microflora plays a crucial role in human health. Furthermore, cholic acid, a major component of bile acid secreted in the intestines, is closely associated with the gut microbiota. While Comamonas testosteroni TA441 is recognized as the leading bacterial model for aerobic steroid degradation, the involvement of aerobic steroid degradation in the intestinal microflora remains largely unexplored. Nonetheless, the presence of C. testosteroni in the cecum suggests the potential influence of aerobic steroid degradation on gut microbiota. To establish essential information about the role of these bacteria, here, we identified the missing compounds and propose more details of C-, and D-ring cleavage, which have remained unclear until now.

Medicines as an emergent contaminant: the review of microbial biodegration potential

Emerging environmental contaminants, such as medicine waste, are of great concern to the scientific community and to the local environmental and health departments because of their potential long-term effects and ecotoxicological risk. Besides the prolonged use of medicines for the development of modern society, the elucidation of their effect on the ecosystem is relatively recent. Medicine waste and its metabolites can, for instance, cause alterations in microbial dynamics and disturb fish behavior. Bioremediation is an efficient and eco-friendly technology that appears as a suitable alternative to conventional methods of water waste and sludge treatment and has the capacity to remove or reduce the presence of emerging contaminants. Thus, this review has the objective of compiling information on environmental contamination by common medicines and their microbial biodegradation, focusing on five therapeutic classes: analgesics, antibiotics, antidepressants, non-steroidal anti-inflammatory drugs (NSAIDs), and contraceptives. Their effects in the environment will also be analyzed, as well as the possible routes of degradation by microorganisms.

Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor

In this work, Caenibius tardaugens NBRC 16725 (strain ARI-1) (formerly Novosphingobium tardaugens) was isolated due to its capacity to mineralize estrogenic endocrine disruptors. Its genome encodes the edc genes cluster responsible for the degradation of 17β-estradiol, consisting of two putative operons (OpA and OpB) encoding the enzymes of the upper degradation pathway. Inside the edc cluster, we identified the edcR gene encoding a TetR-like protein. Genetic studies carried out with C. tardaugens mutants demonstrated that EdcR represses the promoters that control the expression of the two operons. These genetic analyses have also shown that 17β-estradiol and estrone, the second intermediate of the degradation pathway, are the true effectors of EdcR. This regulatory system has been heterologously expressed in Escherichia coli, foreseeing its use to detect estrogens in environmental samples. Genome comparisons have identified a similar regulatory system in the edc cluster of Altererythrobacter estronivorus MHB5, suggesting that this regulatory arrangement has been horizontally transferred to other bacteria.

Identification of the Coenzyme A (CoA) Ester Intermediates and Genes Involved in the Cleavage and Degradation of the Steroidal C-Ring by Comamonas testosteroni TA441

Comamonas testosteroni TA441 degrades steroids aerobically via aromatization of the A-ring accompanied by B-ring cleavage, followed by D- and C-ring cleavage. We previously revealed major enzymes and intermediate compounds in A,B-ring cleavage, the β-oxidation cycle of the cleaved B-ring, and partial C,D-ring cleavage. Here, we elucidate the C-ring cleavage and the β-oxidation cycle that follows. ScdL1L2, a 3-ketoacid coenzyme A (CoA) transferase which belongs to the SugarP_isomerase superfamily, was thought to cleave the C-ring of 9-oxo-1,2,3,4,5,6,10,19-octanor-13,17-secoandrost-8(14)-ene-7,17-dioic acid-CoA ester, the key intermediate compound in the degradation of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (3aα-H-4α [3'-propionic acid]-7aβ-methylhexahydro-1,5-indanedione; HIP)-CoA ester in our previous study; however, the present study suggested that ScdL1L2 is the isomerase of the derivative with a hydroxyl group at C-14 which cleaves the C-ring. The subsequent ring-cleaved product was indicated to be converted to 4-methyl-5-oxo-octane-1,8-dioic acid-CoA ester mainly by ORF33-encoded CoA-transferase (named ScdJ), followed by dehydrogenation by ORF21- and 22-encoded acyl-CoA dehydrogenase (named ScdM1M2). Then, a water molecule is added by ScdN for further degradation by β-oxidation. ScdN is proposed to catalyze the last reaction in C,D-ring degradation by the enzymes encoded in the steroid degradation gene cluster tesB to tesR. IMPORTANCE Studies on bacterial steroid degradation were initiated more than 50 years ago primarily to obtain materials for steroid drugs. Steroid-degrading bacteria are globally distributed, and the role of bacterial steroid degradation in the environment, as well as in humans, is attracting attention. The overall degradation process of the four steroidal rings has been proposed; however, there is still much to be revealed to understand the complete degradation pathway. This study aimed to uncover the whole steroid degradation process in C. testosteroni, which is one of the most studied representative steroid-degrading bacteria and is suitable for exploring the degradation pathway because the involvement of degradation-related genes can be determined by gene disruption.

Characterization of a LuxR repressor for 3,17β-HSD in Comamonas testosteroni ATCC11996

3,17β-Hydroxysteroid dehydrogenase in Comamonas testosteroni (C. testosteroni) is a key enzyme involved in the degradation of steroid compounds. Recently, we found that LuxR is a negative regulator in the expression of the 3,17β-HSD gene. In the present work, we cultured wild-type and LuxR knock-out mutants of C. testosteroni with inducers such as testosterone, estradiol, progesterone or estrone. HPLC analysis showed that the degradation activities towards testosterone, estradiol, progesterone, and estrone by C.T.-LuxR-KO1 were increased by 7.1%, 9.7%, 11.9% and 3.1%, respectively compared to the wild-type strain. Protein conformation of LuxR was predicted by Phyre 2 Server software, where the N-terminal 86(Ile), 116(Ile), 118(Met) and 149(Phe) residues form a testosterone binding hydrophobic pore, while the C-terminus forms the DNA binding site (HTH). Further, luxr point mutant plasmids were prepared by PCR and co-transformed with pUC3.2-4 into E. coli HB101. ELISA was used to determine 3,17β-HSD expression after testosterone induction. Compared to wild-type luxr, 3,17β-HSD expression in mutants of I86T, I116T, M118T and F149S were decreased. The result indicates that testosterone lost its capability to bind to LuxR after the four amino acid residues had been exchanged. No significant changes of 3,17β-HSD expression were found in K354I and Y356 N mutants compared to wild-type luxr, which indicates that these two amino acid residues in LuxR might relate to DNA binding. Native LuxR protein was prepared from inclusion bodies using sodium lauroylsarcosinate. Molecular interaction experiments showed that LuxR protein binds to a nucleotide sequence which locates 87 bp upstream of the βhsd promoter. Our results revealed that steroid induction of 3,17β-HSD in C. testosteroni in fact appears to be a de-repression, where testosterone prevents the LuxR regulator protein binding to the 3,17β-HSD promoter domain.

The characterization of a short chain dehydrogenase/reductase (SDRx) in Comamonas testosteroni

C. testosteroni is a research topic that can degrade steroid hormones into water and carbon dioxide through a series of enzymes in the body. Short-chain dehydrogenase (SDR) are a class of NAD (P) H-dependent oxidoreductases in C. testosteroni. Its main function is catalyzing the redox of the hydroxyl/ketone group of the hormone. In this paper, a SDR gene(SDRx) is cloned from C. testosteroni ATCC11996 and expressed. The polyclonal antibody was prepared and the SDRx gene knocked out by homologous recombination. Wild type and mutant C. testosteroni induced by testosterone, estradiol, estrone and estriol. The growth curves of the bacteria were measured by spectrophotometer. ELISA established the expression of SDRx protein, and high-performance liquid chromatography(HPLC) detected the contents of various hormones. The results show that the growth of wild type was faster than mutant type induced by testosterone. The concentration of SDRx is 0.318 mg/ml under testosterone induction. It has a great change in steroid hormones residue in culture medium measured by HPLC: Testosterone residue in the mutant type group was 42.4 % more than the wild type in culture medium. The same thing happens with induced by estrone. In summary, this SDRx gene involved in the degradation of testosterone and estradiol, and effects the growth of C. testosteroni.

Steroid Degradation in Comamonas testosteroni TA441: Identification of the Entire β-Oxidation Cycle of the Cleaved B Ring

Comamonas testosteroni TA441 degrades steroids via aromatization of the A ring, followed by degradation of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, mainly by β-oxidation. In this study, we revealed that 7β,9α-dihydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostanoic acid-coenzyme A (CoA) ester is dehydrogenated by (3S)-3-hydroxylacyl CoA-dehydrogenase, encoded by scdE (ORF27), and then the resultant 9α-hydroxy-7,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid-CoA ester is converted by 3-ketoacyl-CoA transferase, encoded by scdF (ORF23). With these results, the whole cycle of β-oxidation on the side chain at C-8 of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid is clarified; 9-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid-CoA ester is dehydrogenated at C-6 by ScdC1C2, followed by hydration by ScdD. 7β,9α-Dihydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostanoic acid-CoA ester then is dehydrogenated by ScdE to be converted to 9α-hydroxy-17-oxo-1,2,3,4,5,6,10,19-octanorandrostan-7-oic acid-CoA ester and acetyl-CoA by ScdF. ScdF is an ortholog of FadA6 in Mycobacterium tuberculosis H37Rv, which was reported as a 3-ketoacyl-CoA transferase involved in C ring cleavage. We also obtained results suggesting that ScdF is also involved in C ring cleavage, but further investigation is required for confirmation. ORF25 and ORF26, located between scdF and scdE, encode enzymes belonging to the amidase superfamily. Disrupting either ORF25 or ORF26 did not affect steroid degradation. Among the bacteria having gene clusters similar to those of tesB to tesR, some have both ORF25- and ORF26-like proteins or only an ORF26-like protein, but others do not have either ORF25- or ORF26-like proteins. ORF25 and ORF26 are not crucial for steroid degradation, yet they might provide clues to elucidate the evolution of bacterial steroid degradation clusters.IMPORTANCE Studies on bacterial steroid degradation were initiated more than 50 years ago primarily to obtain materials for steroid drugs. Steroid-degrading bacteria are globally distributed, and the role of bacterial steroid degradation in the environment as well as in relation to human health is attracting attention. The overall aerobic degradation of the four basic steroidal rings has been proposed; however, there is still much to be revealed to understand the complete degradation pathway. This study aims to uncover the whole steroid degradation process in Comamonas testosteroni TA441 as a model of steroid-degrading bacteria. C. testosteroni is one of the most studied representative steroid-degrading bacteria and is suitable for exploring the degradation pathway, because the involvement of degradation-related genes can be determined by gene disruption. Here, we elucidated the entire β-oxidation cycle of the cleaved B ring. This cycle is essential for the following C and D ring cleavage.

Background nutrients and bacterial community evolution determine 13C-17β-estradiol mineralization in lake sediment microcosms

Microbial biodegradation plays a key role in determining the fate of estrogens and can be affected by the background nutrients in natural environments. However, information on how microbial community and nutrient conditions influence estrogen biodegradation is very limited. In this study, ¹³C-17β-estradiol (¹³C-E2) was supplied to sediments from the Central Area (CA), Gonghu (GH), Meiliang (ML), and Zhushan (ZS) Bays of Taihu Lake to investigate shifts in bacterial community structure associated with ¹³C-E2 mineralization over a 30-day incubation period, and the relationships between the background nutrients and cumulative ¹³C-E2 mineralization rates. The cumulative ¹³C-E2 mineralization rate for ZS Bay was 87.40% on Day 30, which was significantly greater (P < 0.05) than the rates for ML Bay (67.74%), GH Bay (62.79%), and the CA (52.60%). A correlation analysis suggested that the cumulative ¹³C-E2 mineralization rate was significantly and positively related to the concentrations of total organic carbon (P < 0.01), nitrate-nitrogen (P < 0.05), ammonia-nitrogen (P < 0.001), and dissolved phosphorus (P < 0.001) in the sediments. Although the highest relative abundances of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes (contain most estrogen-degrading bacteria) were not initially in the ZS Bay sediment, the addition of ¹³C-E2 stimulated their growth in all sediments, with the greatest increases observed for ZS Bay. At the genus level, the cumulative increases of seven genera (Nitrosomonas, Bacillus, Pseudomonas, Sphingomonas, Novosphingobium, Alcaligenes and Mycobacterium) considered to be associated with E2 degradation were also highest for ZS Bay (80.2 times), followed by ML Bay (39.8 times), GH Bay (28.1 times), and CA (19.0 times). Besides the higher nutrient concentrations, the responses of bacteria to ¹³C-E2 addition in ZS Bay could also explain it having the highest cumulative ¹³C-E2 mineralization rate. These results indicate both the background nutrients and bacterial community evolution in the sediments determined the ¹³C-E2 mineralization rates.

Identification of 4-methyl-5-oxo-octane-1,8-dioic acid and the derivatives as metabolites of steroidal C,D-ring degradation in Comamonas testosteroni TA441

Comamonas testosteroni TA441 degrades steroids via 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, which is presumed to be further degraded by β-oxidation. In the β-oxidation process, Coenzyme A (CoA)-ester of 9-oxo-1,2,3,4,5,6,10,19-octanor-13,17-secoandrost-8(14)-ene-7,17-dioic acid is produced and converted by β-ketoacyl-CoA-transferase encoded by ORF1 and ORF2 (scdL1L2) to cleave the remaining C-ring. In this study, we isolated and identified 4-methyl-5-oxo-octane-1,8-dioic acid and 4-methyl-5-oxo-3-octene-1,8-dioic acid from the culture of the ORF3 (scdN)-null mutant as metabolites of steroid degradation (ADD and cholic acid analogues; cholic acid, chenodeoxycholic acid, deoxycholic acid, and lithocholic acid). In addition of these compounds, UHPLC/MS analysis of the culture of the scdN-null mutant revealed significant accumulation of another compound, which was detected as a dominant peak of m/z 155 ([M-CO₂]^-) accompanied by a small peak of parental ion (m/z 199 [M^-]). On the bases of experimental data, this compound was presumed to be 4-methyl-5-oxo-2-octene-1,8-dioic acid, whose CoA-ester was indicated to be converted by scdN-encoded CoA-hydratase into the CoA-ester of 3-hydroxy-4-methyl-5-oxooctan-1,7-carboxylic acid.

Identification of 9-oxo-1,2,3,4,5,6,10,19-octanor-13,17-secoandrost-8(14)-ene-7,17-dioic acid as a metabolite of steroid degradation in Comamonas testosteroni TA441 and the genes involved in the conversion

Comamonas testosteroni TA441 degrades steroid compounds via aromatization of the A-ring to produce 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (a metabolite with C- and D-rings), which is presumed to be further degraded via β-oxidation. In elucidating the complete steroid degradation process in C. testosteroni, we isolated 9-oxo-1,2,3,4,5,6,10,19-octanor-13,17-secoandrost-8(14)-ene-7,17-dioic acid and several other metabolites containing only C-ring. For conversion of the CoA-ester of this compound, a two-subunit β -ketoacyl-CoA-transferase encoded by ORF1 and ORF2 was shown to be indispensable. ORF1 and ORF2 are located just after tesB, the meta-cleavage enzyme gene in one of the two major steroid degradation gene clusters of strain TA441. Conversion by the CoA-transferase leads to cleavage of the remaining C-ring, and the product was suggested to be further degraded by β-oxidation involving other genes in the cluster. ORF1 and ORF2 are considered orthologues of ipdAB gene in Mycobacterium tuberculosis H37Rv, which is recently reported as the CoA-transferase of 9-oxo-1,2,3,4,5,6,10,19-octanor-13,17-secoandrost-8(14)-ene-7,17-dioic acid (Crowe AM, Casabon I, Brown KL, Liu J, Lian J, Rogalski JC, Hurst TE, Snieckus V, Foster LJ, Eltis LD. 2017. MBio 8).

Steroid Degradation in Comamonas testosteroni TA441: Identification of Metabolites and the Genes Involved in the Reactions Necessary before D-Ring Cleavage

Bacterial steroid degradation has been studied mainly with Rhodococcus equi (Nocardia restrictus) and Comamonas testosteroni as representative steroid degradation bacteria for more than 50 years. The primary purpose was to obtain materials for steroid drugs, but recent studies showed that many genera of bacteria (Mycobacterium, Rhodococcus, Pseudomonas, etc.) degrade steroids and that steroid-degrading bacteria are globally distributed and found particularly in wastewater treatment plants, the soil, plant rhizospheres, and the marine environment. The role of bacterial steroid degradation in the environment is, however, yet to be revealed. To uncover the whole steroid degradation process in a representative steroid-degrading bacterium, C. testosteroni, to provide basic information for further studies on the role of bacterial steroid degradation, we elucidated the two indispensable oxidative reactions and hydration before D-ring cleavage in C. testosteroni TA441. In bacterial oxidative steroid degradation, A- and B-rings of steroids are cleaved to produce 2-hydroxyhexa-2,4-dienoic acid and 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid. The latter compound was revealed to be degraded to the coenzyme A (CoA) ester of 9α-hydroxy-17-oxo-1,2,3,4,5,6,10,19-octanorandrostan-7-oic acid, which is converted to the CoA ester of 9,17-dioxo-1,2,3,4,5,6,10,19-octanorandrostan-7-oic acid by ORF31-encoded hydroxylacyl dehydrogenase (ScdG), followed by conversion to the CoA ester of 9,17-dioxo-1,2,3,4,5,6,10,19-octanorandrost-8(14)-en-7-oic acid by ORF4-encoded acyl-CoA dehydrogenase (ScdK). Then, a water molecule is added by the ORF5-encoded enoyl-CoA hydratase (ScdY), which leads to the cleavage of the D-ring. The conversion by ScdG is presumed to be a reversible reaction. The elucidated pathway in C. testosteroni TA441 is different from the corresponding pathways in Mycobacterium tuberculosis H37Rv.IMPORTANCE Studies on representative steroid degradation bacteria Rhodococcus equi (Nocardia restrictus) and Comamonas testosteroni were initiated more than 50 years ago primarily to obtain materials for steroid drugs. A recent study showed that steroid-degrading bacteria are globally distributed and found particularly in wastewater treatment plants, the soil, plant rhizospheres, and the marine environment, but the role of bacterial steroid degradation in the environment is yet to be revealed. This study aimed to uncover the whole steroid degradation process in C. testosteroni TA441, in which major enzymes for steroidal A- and B-ring cleavage were elucidated, to provide basic information for further studies on bacterial steroid degradation. C. testosteroni is suitable for exploring the degradation pathway because the involvement of degradation-related genes can be determined by gene disruption. We elucidated the two indispensable oxidative reactions and hydration before D-ring cleavage, which appeared to differ from those present in Mycobacterium tuberculosis H37Rv.

Biodegradation of 17β-estradiol by Bacterial Co-culture Isolated from Manure

Animal wastes are potential sources of natural and steroidal estrogen hormones into the environment. These hormones can be removed by microorganisms with induced enzymes. Two strains of 17β-estradiol-degrading bacteria (LM1 and LY1) were isolated from animal wastes. Based on biochemical characteristics and 16 S rDNA gene sequences, we identified strains LM1 and LY1 as belonging to the genus of Acinetobacter and Pseudomonas, respectively. Bacterial co-culture containing LM1 and LY1 bacterial strains could rapidly remove approximately 98% of E2 (5 mg L⁻¹) within 7 days. However, strains LM1 and LY1 degraded 77% and 68% of E2 when they were incubated alone, respectively. More than 90% of 17β-estradiol (E2, ≤ 20 mg L⁻¹) could be removed by bacterial co-culture. Low C/N ratio (1:35) was more suitable for bacterial growth and E2 degradation. The optimal pH for bacterial co-culture to degrade E2 ranged from 7.00 to 9.00. Coexisting sodium acetate, glucose and sodium citrate decreased E2 degradation in the first 4 days, but more E2 was removed when they were depleted. The growth of the bacterial co-culture was not significantly decreased by Ni, Pb, Cd or Cu at or below 0.8, 1.2, 1.6 or 0.8 mg L⁻¹, respectively. These data highlight the usefulness of bacterial co-culture in the bioremediation of estrogen-contaminated environments.

Functional analysis of a novel repressor LuxR in Comamonas testosteroni

Comamonas testosteroni (C. testosteroni) ATCC11996 is a gram negative bacterium which can use steroid as a carbon and energy source. 3,17β-hydroxysteroid dehydrogenase (3,17β-HSD) is a key enzyme for the degradation of steroid hormones in C. testosteroni. The LuxR regulation family is a group of regulatory proteins which play important role in gram negative bacterium. The luxr gene is located on 58 kb upstream of 3,17β-HSD gene with the opposite transcription orientation in the chromosomal DNA of C. testosteroni. An open reading frame of this putative luxr gene consists of 1125 bp and is translated into a protein containing 374 amino acids. The luxr gene was cloned into plasmid pK18 and plasmid pK-LuxR1 was obtained. E. coli HB101 was co-transformed by pK-LuxR1 and pUC912-10, pUC1128-5 or pUC3.2-4 (which contain βhsd gene and different length promoter, repeat sequences). The result of ELISA showed that LuxR protein is a negative regulator for 3,17β-HSD expression. The luxr gene in C. testosteroni was knock-out by homologous integration. 3,17β-HSD expression was increased in the mutant (C.T.-L-KO1) comparing to that in wild-type C. testosteroni (C.T.) after 0.5 mM testosterone induction. The mutant C.T.-L-KO1 and wild-type C. testosteroni were cultured at 27 °C and 37 °C. The result of growth curve proved that LuxR has also effect on the bacterial growth.

Identification and isolation of a regulator protein for 3,17β-HSD expressional regulation in Comamonas testosteroni

Comamonas testosteroni (C. testosteroni) is able to catabolize a variety of steroids and polycyclic aromatic hydrocarbons. 3,17β-Hydroxysteroid dehydrogenase (3,17β-HSD) from C. testosteroni is a member of the short-chain dehydrogenase/reductase (SDR) superfamily. It is an inducible and key enzyme in steroid degradation. Elucidating the mechanism of 3,17β-HSD gene (βhsd) regulation may help us to generate prospective C. testosteroni mutants for bioremediation. The genome of C. testosteroni ATCC11996 was sequenced in our previous work. Upon examining the genome with bioinformatics tools, a gene (brp) coding for a regulator protein (BRP) for 3,17β-HSD expression was found upstream of the βhsd gene. A Blast search revealed high identities to a nucleotide binding protein with unknown function in other bacteria. Two potential promoters and two repeat sequences (RS, 16 bp), spaced to each other by 1661 bp, were also found upstream of the βhsd gene C. testosteroni. The brp gene was cloned into plasmid pK18 and pET-15b, expressed in Escherichia coli, and the recombinant BRP protein was purified on a Ni-column. In addition, a brp gene knock-out mutant of C. testosteroni was prepared. These knock-out mutants showed an enhanced expression of both the βhsd gene and the hsdA gene (the latter coding for 3α-HSD/CR) in the presence of testosterone. To characterize the BRP functional DNA domain, different fragments of the βhsd upstream regulatory region were tested in a cotransformation system. Our data reveal that the βhsd gene undergoes complex regulation involving the two promoters, a loop structure via the two repeat sequences, and the steroid testosterone. Furthermore, a proximal repressor gene for βhsd expression, phaR, had been identified in our previous investigations. The exact interplay between all these factors will be determined in future experiments.

Isolation and identification of a repressor TetR for 3,17β-HSD expressional regulation in Comamonas testosteroni

Comamonas testosteroni (C. testosteroni) is able to catabolize a variety of steroids and polycyclic aromatic hydrocarbons. 3,17β-Hydroxysteroid dehydrogenase (3,17β-HSD) from C. testosteroni is a key enzyme in steroid degradation. Understanding the mechanism of 3,17β-HSD gene (βhsd) induction may help us to elucidate its complete molecular regulation. Sequencing the C. testosteroni ATCC11996 genome lead us to identify the tetR (522 bp) downstream of βhsd. Two repeat sequences (RS; 13 bp), that are separated to each other by 1661 bp, were found upstream of βhsd. A bioinformatic analysis revealed that TetR family proteins act as transcriptional repressors which are sensitive to environmental signals. Since, C. testosteroni responds to environmental steroid induction and upregulates steroid catabolic genes, we hypothesized that TetR might act in C. testosteroni as repressor for βhsd expression. The tetR was cloned into different plasmids, including an EGFP reporter system, for functional characterization and/or overexpression. The data indicate that, indeed, TetR acts as a repressor for 3,17β-HSD expression. Testosterone in turn, which is known to induce βhsd expression, could not resolve TetR repression. To further substantiate TetR as repressor for βhsd expression, a tetR gene knock-out mutant of C. testosteroni was generated. TetR gene knock-out mutants showed the same basal low level of βhsd expression as the C. testosteroni wild type cells. Interestingly, testosterone induction leads to a strong increase in βhsd expression, especially in the tetR gene knock-out mutants. The result with the knock-out mutant, in principle, supports our hypothesis that TetR is a repressor for βhsd expression, but the exact role of testosterone in this context remains unknown. Finally, it turned out that TetR is obviously also involved in the regulation of the hsdA gene.

Steroid degradation in Comamonas testosteroni

Steroid degradation by Comamonas testosteroni and Nocardia restrictus have been intensively studied for the purpose of obtaining materials for steroid drug synthesis. C. testosteroni degrades side chains and converts single/double bonds of certain steroid compounds to produce androsta-1,4-diene 3,17-dione or the derivative. Following 9α-hydroxylation leads to aromatization of the A-ring accompanied by cleavage of the B-ring, and aromatized A-ring is hydroxylated at C-4 position, cleaved at Δ4 by meta-cleavage, and divided into 2-hydroxyhexa-2,4-dienoic acid (A-ring) and 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (B,C,D-ring) by hydrolysis. Reactions and the genes involved in the cleavage and the following degradation of the A-ring are similar to those for bacterial biphenyl degradation, and 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid degradation is suggested to be mainly β-oxidation. Genes involved in A-ring aromatization and degradation form a gene cluster, and the genes involved in β-oxidation of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid also comprise a large cluster of more than 10 genes. The DNA region between these two main steroid degradation gene clusters contain 3α-hydroxysteroid dehydrogenase gene, Δ5,3-ketosteroid isomerase gene, genes for inversion of an α-oriented-hydroxyl group to a β-oriented-hydroxyl group at C-12 position of cholic acid, and genes possibly involved in the degradation of a side chain at C-17 position of cholic acid, indicating this DNA region of more than 100kb to be a steroid degradation gene hot spot of C. testosteroni. Article from a special issue on steroids and microorganisms.

Hydroxysteroid dehydrogenases (HSDs) in bacteria: a bioinformatic perspective

Steroidal compounds including cholesterol, bile acids and steroid hormones play a central role in various physiological processes such as cell signaling, growth, reproduction, and energy homeostasis. Hydroxysteroid dehydrogenases (HSDs), which belong to the superfamily of short-chain dehydrogenases/reductases (SDR) or aldo-keto reductases (AKR), are important enzymes involved in the steroid hormone metabolism. HSDs function as an enzymatic switch that controls the access of receptor-active steroids to nuclear hormone receptors and thereby mediate a fine-tuning of the steroid response. The aim of this study was the identification of classified functional HSDs and the bioinformatic annotation of these proteins in all complete sequenced bacterial genomes followed by a phylogenetic analysis. For the bioinformatic annotation we constructed specific hidden Markov models in an iterative approach to provide a reliable identification for the specific catalytic groups of HSDs. Here, we show a detailed phylogenetic analysis of 3α-, 7α-, 12α-HSDs and two further functional related enzymes (3-ketosteroid-Δ(1)-dehydrogenase, 3-ketosteroid-Δ(4)(5α)-dehydrogenase) from the superfamily of SDRs. For some bacteria that have been previously reported to posses a specific HSD activity, we could annotate the corresponding HSD protein. The dominating phyla that were identified to express HSDs were that of Actinobacteria, Proteobacteria, and Firmicutes. Moreover, some evolutionarily more ancient microorganisms (e.g., Cyanobacteria and Euryachaeota) were found as well. A large number of HSD-expressing bacteria constitute the normal human gastro-intestinal flora. Another group of bacteria were originally isolated from natural habitats like seawater, soil, marine and permafrost sediments. These bacteria include polycyclic aromatic hydrocarbons-degrading species such as Pseudomonas, Burkholderia and Rhodococcus. In conclusion, HSDs are found in a wide variety of microorganisms including bacteria and archaea, suggesting that steroid metabolism is an evolutionarily conserved mechanism that might serve different functions such as nutrient supply and signaling. Article from a special issue on steroids and microorganisms.

New microbiological transformations of steroids by Streptomyces virginiae IBL-14

A bacterium Streptomyces virginiae IBL-14 capable of effective degradation of diosgenin was isolated from activated sludge for treatment of waste from a steroidal drug factory. From the culture broth of diosgenin degradation, 11 compounds were purified and then identified, eight of which were previously unidentified compounds including 1-dehydroisonuatigenone [VI], nuatigenone [VIII], 1-dehydronuatigenone [X], 26-acetyl-nuatigenone [XII], 6-methoxy-6-dehydrodiosgenone [XIII], 6-methoxy-6-dehydroisonuatigenone [XIV], 6-methoxy-6-dehydronuatigenone [XV], and 6-dimethoxy-7alpha-hydroxyldiosgenone [XVI]. Additionally, two important microbial transformations of diosgenin (6-methoxylation and C25-tertiary carbon hydroxylation) were found. Two valuable chemical reactions of the steroids (structural rearrangement and esterification)were also confirmed. As a result, a new metabolic pathway of diosgenin metabolism was postulated.

Regulation of testosterone degradation in Comamonas testosteroni

Recently, we have identified a gene encoding a LuxR-type factor, TeiR (Testosterone-inducible Regulator), which positively regulates steroid degradation in Comamonas testosteroni. Herein, we demonstrate that TeiR interacts in vivo with steroid catabolic gene promoters. The presence of testosterone induces a significant TeiR protein increase at the early logarithmic phase of growth. Interestingly, it is not until the early stationary phase where the activation of a steroid-inducible gene promoter is observed, indicating that testosterone might not be the true inductor of the steroid degradation pathway. In addition, beta-galactosidase expression driven by a testosterone-inducible promoter is prematurely activated in cells cultured in medium supplemented with ethyl acetate extracts obtained from the early stationary phase cell-free supernatants of C. testosteroni grown in presence of testosterone. Complementation experiments of C. testosteroni wild type performed with teiR deletion constructs indicate that extra-copies of deleted-TeiR exert a dominant negative effect on the wild-type TeiR protein. While, when C. testosteroni teiR mutants were used to carry out complementation assays only the full length gene can overcome the teiR mutant phenotype. Altogether these findings indicate that TeiR regulates steroid catabolic genes interacting with their promoters and suggest that this interaction requires the presence of a testosterone-derived metabolite to induce the system.