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Fufaeva SR, Dovbnya DV, Ivashina TV, Shutov AA, Donova MV. Reconstruction of the Steroid 1(2)-Dehydrogenation System from Nocardioides simplex VKM Ac-2033D in Mycolicibacterium Hosts. Microorganisms 2023; 11:2720. [PMID: 38004731 PMCID: PMC10672877 DOI: 10.3390/microorganisms11112720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Microbial 1(2)-dehydrogenation of 3-ketosteroids is an important basis for the production of many steroid pharmaceuticals and synthons. When using the wild-type strains for whole cell catalysis, the undesirable reduction of the 20-carbonyl group, or 1(2)-hydrogenation, was observed. In this work, the recombinant strains of Mycolicibacterium neoaurum and Mycolicibacterium smegmatis were constructed with blocked endogenous activity of 3-ketosteroid-9α-hydroxylase, 3-ketosteroid-1(2)-dehydrogenase (3-KSD), and expressing 3-KSD encoded by the gene KR76_27125 (kstD2NS) from Nocardioides simplex VKM Ac-2033D. The in vivo activity of the obtained recombinant strains against phytosterol, 6α-methyl-hydrocortisone, and hydrocortisone was studied. When using M. smegmatis as the host strain, the 1(2)-dehydrogenation activity of the constructed recombinant cells towards hydrocortisone was noticeably higher compared to those on the platform of M. neoaurum. A comparison of the strengths of inducible acetamidase and constitutive hsp60 promoters in M. smegmatis provided comparable results. Hydrocortisone biotransformation by M. smegmatis BD/pMhsp_k expressing kstD2NS resulted in 95.4% prednisolone yield, and the selectivity preferred that for N. simplex. Mycolicibacteria showed increased hydrocortisone degradation at 35 °C compared to 30 °C. The presence of endogenous steroid catabolism in Mycolicibacterium hosts does not seem to confer an advantage for the functioning of KstD2NS. The results allow for the evaluation of the prospects for the development of simple technological methods for the selective 1(2)-dehydrogenation of 3-ketosteroids by growing bacterial cells.
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Affiliation(s)
| | | | | | | | - Marina V. Donova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (S.R.F.); (D.V.D.); (T.V.I.); (A.A.S.)
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2
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Kim Tiam S, Boubakri H, Bethencourt L, Abrouk D, Fournier P, Herrera-Belaroussi A. Genomic Insights of Alnus-Infective Frankia Strains Reveal Unique Genetic Features and New Evidence on Their Host-Restricted Lifestyle. Genes (Basel) 2023; 14:530. [PMID: 36833457 PMCID: PMC9956245 DOI: 10.3390/genes14020530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 02/23/2023] Open
Abstract
The present study aimed to use comparative genomics to explore the relationships between Frankia and actinorhizal plants using a data set made of 33 Frankia genomes. The determinants of host specificity were first explored for "Alnus-infective strains" (i.e., Frankia strains belonging to Cluster Ia). Several genes were specifically found in these strains, including an agmatine deiminase which could possibly be involved in various functions as access to nitrogen sources, nodule organogenesis or plant defense. Within "Alnus-infective strains", Sp+ Frankia genomes were compared to Sp- genomes in order to elucidate the narrower host specificity of Sp+ strains (i.e., Sp+ strains being capable of in planta sporulation, unlike Sp- strains). A total of 88 protein families were lost in the Sp+ genomes. The lost genes were related to saprophytic life (transcriptional factors, transmembrane and secreted proteins), reinforcing the proposed status of Sp+ as obligatory symbiont. The Sp+ genomes were also characterized by a loss of genetic and functional paralogs, highlighting a reduction in functional redundancy (e.g., hup genes) or a possible loss of function related to a saprophytic lifestyle (e.g., genes involved in gas vesicle formation or recycling of nutrients).
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Affiliation(s)
- Sandra Kim Tiam
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
- UMR CNRS 5557 Ecologie Microbienne, INRA UMR 1418, Centre d’Etude des Substances Naturelles, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Lorine Bethencourt
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Danis Abrouk
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Aude Herrera-Belaroussi
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
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Wójcik P, Glanowski M, Mrugała B, Procner M, Zastawny O, Flejszar M, Kurpiewska K, Niedziałkowska E, Minor W, Oszajca M, Bojarski AJ, Wojtkiewicz AM, Szaleniec M. Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Δ 1-Dehydrogenase from Sterolibacterium denitrificans─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis. Biochemistry 2023; 62:808-823. [PMID: 36625854 PMCID: PMC9960185 DOI: 10.1021/acs.biochem.2c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenases (KstD) are important microbial flavin enzymes that initiate the metabolism of steroid ring A and find application in the synthesis of steroid drugs. We present a structure of the KstD from Sterolibacterium denitrificans (AcmB), which contains a previously uncharacterized putative membrane-associated domain and extended proton-relay system. The experimental and theoretical studies show that the steroid Δ1-dehydrogenation proceeds according to the Ping-Pong bi-bi kinetics and a two-step base-assisted elimination (E2cB) mechanism. The mechanism is validated by evaluating the experimental and theoretical kinetic isotope effect for deuterium-substituted substrates. The role of the active-site residues is quantitatively assessed by point mutations, experimental activity assays, and QM/MM MD modeling of the reductive half-reaction (RHR). The pre-steady-state kinetics also reveals that the low pH (6.5) optimum of AcmB is dictated by the oxidative half-reaction (OHR), while the RHR exhibits a slight optimum at the pH usual for the KstD family of 8.5. The modeling confirms the origin of the enantioselectivity of C2-H activation and substrate specificity for Δ4-3-ketosteroids. Finally, the cholest-4-en-3-one turns out to be the best substrate of AcmB in terms of ΔG of binding and predicted rate of dehydrogenation.
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Affiliation(s)
- Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland; Jerzy Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Olga Zastawny
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Monika Flejszar
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland; Department of Physical Chemistry, Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland
| | | | - Ewa Niedziałkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University,30-387 Kraków, Poland
| | - Andrzej J. Bojarski
- Jerzy Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Agnieszka M. Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
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Wojtkiewicz AM, Glanowski M, Waligórski P, Janeczko T, Szaleniec M. 1,2-Hydrogenation and Transhydrogenation Catalyzed by 3-Ketosteroid Δ 1-Dehydrogenase from Sterolibacterium denitrificans-Kinetics, Isotope Labelling and QM:MM Modelling Studies. Int J Mol Sci 2022; 23:14660. [PMID: 36498984 PMCID: PMC9736390 DOI: 10.3390/ijms232314660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria and fungi that are able to metabolize steroids express 3-ketosteroid-Δ1-dehydrogenases (KstDs). KstDs such as AcmB form Sterolibacterium denitrificans Chol-1 catalyze the enantioselective 1α,2β-dehydrogenation of steroids to their desaturated analogues, e.g., the formation of 1,4-androstadiene-3,17-dione (ADD) from 4-androsten-3,17-dione (AD). The reaction catalyzed by KstD can be reversed if the appropriate electron donor, such as benzyl viologen radical cation, is present. Furthermore, KstDs can also catalyze transhydrogenation, which is the transfer of H atoms between 3-ketosteroids and 1-dehydrosteroids. In this paper, we showed that AcmB exhibits lower pH optima for hydrogenation and dehydrogenation by 3.5-4 pH units than those observed for KstD from Nocardia corallina. We confirmed the enantiospecificity of 1α,2β-hydrogenation and 1α,2β-transhydrogenation catalyzed by AcmB and showed that, under acidic pH conditions, deuterons are introduced not only at 2β but also at the 1α position. We observed a higher degree of H/D exchange at Y363, which activates the C2-H bond, compared to that at FAD, which is responsible for redox at the C1 position. Furthermore, for the first time, we observed the introduction of the third deuteron into the steroid core. This effect was explained through a combination of LC-MS experiments and QM:MM modelling, and we attribute it to a decrease in the enantioselectivity of C2-H activation upon the deuteration of the 2β position. The increase in the activation barrier resulting from isotopic substitution increases the chance of the formation of d3-substituted 3-ketosteroids. Finally, we demonstrate a method for the synthesis of 3-ketosteroids chirally deuterated at 1α,2β positions, obtaining 1α,2β-d2-4-androsten-3,17-dione with a 51% yield (8.61 mg).
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Affiliation(s)
- Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Piotr Waligórski
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Tomasz Janeczko
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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Focused mutagenesis in non-catalytic cavity for improving catalytic efficiency of 3-ketosteroid-Δ1-dehydrogenase. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ivshina I, Bazhutin G, Tyumina E. Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future. Front Microbiol 2022; 13:967127. [PMID: 36246215 PMCID: PMC9557007 DOI: 10.3389/fmicb.2022.967127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.
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Liang X, Li Y, Tang S, Shi X, Zhou N, Liu K, Ma J, Yu F, Li Y. Mechanism underlying how a chitosan-based phosphorus adsorbent alleviates cadmium-induced oxidative stress in Bidens pilosa L. and its impact on soil microbial communities: A field study. CHEMOSPHERE 2022; 295:133943. [PMID: 35150697 DOI: 10.1016/j.chemosphere.2022.133943] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
In the present study, field experiments were conducted in Side village, Yangshuo, Guilin, Guangxi Province, China, using four C-BPA application levels (control (0 mg m-2), T1 (100 mg m-2), T2 (200 mg m-2) and T3 (400 mg m-2)) to clarify the mechanism by which a chitosan-based phosphorus adsorbent (C-BPA) applied as a passivator helps Bidens pilosa L. (B. pilosa L.) alleviate cadmium (Cd)-induced oxidative stress in Cd-contaminated soil. In the aqueous phase, C-BPA successfully adsorbed Cd2+ on the surface primarily via ion exchange, and C-BPA has potential Cd2+ adsorption capacity, enabling its use as a passivator in real Cd-contaminated environments. In Cd-contaminated soils, under C-BPA application at the T3 level, the pH value increased by 11.2%, and the acid-soluble form of Cd decreased by 26.5%. Additionally, the application of C-BPA improved the rhizosphere soil environment and impacted the soil microbial community diversity and structure. Among soil microbes, the soil fungal community was more sensitive than bacteria to C-BPA application. Dehydrogenase, acetic acid, soil pH and Eurotiomycetes or Dothideomycetes significantly impacted Cd accumulation in the leaves of B. pilosa L.; Cd accumulation in leaves was decreased by 68.1% under C-BPA application at the T3 level. Additionally, the variation of increased catalase (CAT) and peroxidase (POD) jointly promoted plant growth; the plant weight was increased by 112.7% under the C-BPA application at the T3 level. Notably, the production of CAT and POD by B. pilosa L. was more effective than the synthesis of glutathione (GSH) in helping B. pilosa L. eliminate excess reactive oxygen species (ROS). Therefore, our findings demonstrated that the application of C-BPA to Cd-contaminated soil can greatly improve the rhizosphere soil environment, help B. pilosa L. eliminate ROS and promote plant growth.
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Affiliation(s)
- Xin Liang
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Yanying Li
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Shuting Tang
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Xinwei Shi
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Nuobao Zhou
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, 541004, Guilin, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, 541004, Guilin, China
| | - Jiangming Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, 541004, Guilin, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, 541004, Guilin, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China.
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China.
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Wang Y, Zhang R, Feng J, Wu Q, Zhu D, Ma Y. A New 3-Ketosteroid-Δ1–Dehydrogenase with High Activity and Broad Substrate Scope for Efficient Transformation of Hydrocortisone at High Substrate Concentration. Microorganisms 2022; 10:microorganisms10030508. [PMID: 35336084 PMCID: PMC8950399 DOI: 10.3390/microorganisms10030508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022] Open
Abstract
3-Ketosteroid-Δ1-dehydrogenases (KstDs [EC 1.3.99.4]) catalyze the Δ1-dehydrogenation of steroids and are a class of important enzymes for steroid biotransformations. In this study, nine putative kstD genes from different origins were selected and overexpressed in Escherichia coli BL21(DE3). These recombinant enzymes catalyzed the Δ1-desaturation of a variety of steroidal compounds. Among them, the KstD from Propionibacterium sp. (PrKstD) displayed the highest specific activity and broad substrate spectrum. The detailed catalytic characterization of PrKstD showed that it can convert a wide range of 3-ketosteroid compounds with diverse substituents, ranging from substituents at the C9, C10, C11 and C17 position through substrates without C4-C5 double bond, to previously inactive C6-substituted ones such as 11β,17-dihydroxy-6α-methyl-pregn-4-ene-3,20-dione. Reaction conditions were optimized for the biotransformation of hydrocortisone in terms of pH, temperature, co-solvent and electron acceptor. By using 50 g/L wet resting E. coli cells harboring PrKstD enzyme, the conversion of hydrocortisone was about 92.5% within 6 h at the substrate concentration of 80 g/L, much higher than the previously reported results, demonstrating the application potential of this new KstD.
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Mao S, Sun J, Wang L, Gao X, Liu X, Lu F, Qin HM. Mining and characterization of 3-ketosteroid-∆1-dehydrogenases from Arthrobacter simplex genome and applications for steroid dehydrogenation. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yamamoto T, Hasegawa Y, Lau PCK, Iwaki H. Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369. J Biosci Bioeng 2021; 132:621-629. [PMID: 34583900 DOI: 10.1016/j.jbiosc.2021.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/18/2022]
Abstract
Cyclohexanecarboxylate (CHCA) is formed by oxidative microbial degradation of n-alkylcycloparaffins and anaerobic degradation of benzoate, and also known to be a synthetic intermediate or the starter unit of biosynthesis of cellular constituents and secondary metabolites. Although two degradation pathways have been proposed, genetic information has been limited to the β-oxidation-like pathway. In this study, we identified a gene cluster, designated chcC1XTC2B1B2RAaAbAc, that is responsible for the CHCA aromatization pathway in Sinomonas (formerly Corynebacterium) cyclohexanicum strain ATCC 51369. Reverse transcription-PCR analysis indicated that the chc gene cluster is inducible by CHCA and that it consists of two transcriptional units, chcC1XTC2B1B2R and chcAaAbAc. Overexpression of the various genes in Escherichia coli, and purification of the recombinant proteins led to the functional characterization of ChcAaAbAc as subunits of a cytochrome P450 system responsible for CHCA hydroxylation; ChcB1 and ChcB2 as trans-4-hydroxyCHCA and cis-4-hydroxyCHCA dehydrogenases, respectively; ChcC1 was identified as a 4-oxoCHCA desaturase containing a covalently bound FAD; and ChcC2 was identified as a 4-oxocyclohexenecarboxylate desaturase. The binding constant of ChcAa for CHCA was found to be 0.37 mM. Kinetic parameters established for ChcB1 indicated that it has a high catalytic efficiency towards 4-oxoCHCA compared to trans- or cis-4-hydroxyCHCA. The Km and Kcat values of ChcC1 for 4-oxoCHCA were 0.39 mM and 44 s-1, respectively. Taken together with previous work on the identification of a pobA gene encoding a 4-hydroxybenzoate hydroxylase, we have now localized the remaining set of genes for the final degradation of protocatechuate before entry into the tricarboxylic acid cycle.
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Affiliation(s)
- Taisei Yamamoto
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshie Hasegawa
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Peter C K Lau
- Department of Microbiology & Immunology, McGill University, Montréal, Québec, H3A 2B4, Canada
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan.
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11
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Feller FM, Holert J, Yücel O, Philipp B. Degradation of Bile Acids by Soil and Water Bacteria. Microorganisms 2021; 9:1759. [PMID: 34442838 PMCID: PMC8399759 DOI: 10.3390/microorganisms9081759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Bile acids are surface-active steroid compounds with a C5 carboxylic side chain at the steroid nucleus. They are produced by vertebrates, mainly functioning as emulsifiers for lipophilic nutrients, as signaling compounds, and as an antimicrobial barrier in the duodenum. Upon excretion into soil and water, bile acids serve as carbon- and energy-rich growth substrates for diverse heterotrophic bacteria. Metabolic pathways for the degradation of bile acids are predominantly studied in individual strains of the genera Pseudomonas, Comamonas, Sphingobium, Azoarcus, and Rhodococcus. Bile acid degradation is initiated by oxidative reactions of the steroid skeleton at ring A and degradation of the carboxylic side chain before the steroid nucleus is broken down into central metabolic intermediates for biomass and energy production. This review summarizes the current biochemical and genetic knowledge on aerobic and anaerobic degradation of bile acids by soil and water bacteria. In addition, ecological and applied aspects are addressed, including resistance mechanisms against the toxic effects of bile acids.
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Affiliation(s)
- Franziska Maria Feller
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
| | - Onur Yücel
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany
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12
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Li X, Chen T, Peng F, Song S, Yu J, Sidoine DN, Cheng X, Huang Y, He Y, Su Z. Efficient conversion of phytosterols into 4-androstene-3,17-dione and its C1,2-dehydrogenized and 9α-hydroxylated derivatives by engineered Mycobacteria. Microb Cell Fact 2021; 20:158. [PMID: 34399754 PMCID: PMC8365914 DOI: 10.1186/s12934-021-01653-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
4-Androstene-3,17-dione (4-AD), 1,4-androstadiene-3,17-dione (ADD) and 9α-hydroxyl-4-androstene-3,17-dione (9OH-AD), which are important starting compounds for the synthesis of steroidal medicines, can be biosynthetically transformed from phytosterols by Mycobacterium strains. Genomic and metabolic analyses have revealed that currently available 4-AD-producing strains maintain the ability to convert 4-AD to ADD and 9OH-AD via 3-ketosteroid-1,2-dehydrogenase (KstD) and 3-ketosteroid-9α-hydroxylase (Ksh), not only lowering the production yield of 4-AD but also hampering its purification refinement. Additionally, these 4-AD industrial strains are excellent model strains to construct ADD- and 9OH-AD-producing strains. We recently found that Mycobacterium neoaurum HGMS2, a 4-AD-producing strain, harbored fewer kstd and ksh genes through whole-genomic and enzymatic analyses, compared with other strains (Wang et al. in Microbial Cell Fact 19:187, 2020). In this study, we attempted to construct an efficient 4-AD-producing strain by knocking out the kstd and ksh genes from the M. neoaurum HGMS2 strain. Next, we used kstd- and ksh-default HGMS2 mutants as templates to construct ADD- and 9OH-AD-producing strains by knocking in active kstd and ksh genes, respectively. We found that after knocking out its endogenous kstd and ksh genes, one of these knockout mutants, HGMS2Δkstd211 + ΔkshB122, showed a 20% increase in the rate of phytosterol to 4-AD conversion, compared relative to the wild-type strain and an increase in 4-AD yield to 38.3 g/L in pilot-scale fermentation. Furthermore, we obtained the ADD- and 9OH-AD-producing strains, HGMS2kstd2 + Δkstd211+ΔkshB122 and HGMS2kshA51 + Δkstd211+ΔkshA226, by knocking in heterogenous active kstd and ksh genes to selected HGMS2 mutants, respectively. During pilot-scale fermentation, the conversion rates of the ADD- and 9OH-AD-producing mutants transforming phytosterol were 42.5 and 40.3%, respectively, and their yields reached 34.2 and 37.3 g/L, respectively. Overall, our study provides efficient strains for the production of 4-AD, ADD and 9OH-AD for the pharmaceutical industry and provides insights into the metabolic engineering of the HGMS2 strain to produce other important steroidal compounds.
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Affiliation(s)
- Xin Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Tian Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Fei Peng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Shikui Song
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Jingpeng Yu
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Douanla Njimeli Sidoine
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China
| | - Yijun He
- Hubei Goto Biotech Inc., No. 1 Baiguoshu Road, Shuidu Industrial Park, Danjiangkou, 442700, Hubei, China.
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China.
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Wójcik P, Glanowski M, Wojtkiewicz AM, Rohman A, Szaleniec M. Universal capability of 3-ketosteroid Δ 1-dehydrogenases to catalyze Δ 1-dehydrogenation of C17-substituted steroids. Microb Cell Fact 2021; 20:119. [PMID: 34162386 PMCID: PMC8220720 DOI: 10.1186/s12934-021-01611-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 3-Ketosteroid Δ1-dehydrogenases (KSTDs) are the enzymes involved in microbial cholesterol degradation and modification of steroids. They catalyze dehydrogenation between C1 and C2 atoms in ring A of the polycyclic structure of 3-ketosteroids. KSTDs substrate spectrum is broad, even though most of them prefer steroids with small substituents at the C17 atom. The investigation of the KSTD's substrate specificity is hindered by the poor solubility of the hydrophobic steroids in aqueous solutions. In this paper, we used 2-hydroxpropyl-β-cyclodextrin (HBC) as a solubilizing agent in a study of the KSTDs steady-state kinetics and demonstrated that substrate bioavailability has a pivotal impact on enzyme specificity. RESULTS Molecular dynamics simulations on KSTD1 from Rhodococcus erythropolis indicated no difference in ΔGbind between the native substrate, androst-4-en-3,17-dione (AD; - 8.02 kcal/mol), and more complex steroids such as cholest-4-en-3-one (- 8.40 kcal/mol) or diosgenone (- 6.17 kcal/mol). No structural obstacle for binding of the extended substrates was also observed. Following this observation, our kinetic studies conducted in the presence of HBC confirmed KSTD1 activity towards both types of steroids. We have compared the substrate specificity of KSTD1 to the other enzyme known for its activity with cholest-4-en-3-one, KSTD from Sterolibacterium denitrificans (AcmB). The addition of solubilizing agent caused AcmB to exhibit a higher affinity to cholest-4-en-3-one (Ping-Pong bi bi KmA = 23.7 μM) than to AD (KmA = 529.2 μM), a supposedly native substrate of the enzyme. Moreover, we have isolated AcmB isoenzyme (AcmB2) and showed that conversion of AD and cholest-4-en-3-one proceeds at a similar rate. We demonstrated also that the apparent specificity constant of AcmB for cholest-4-en-3-one (kcat/KmA = 9.25∙106 M-1 s-1) is almost 20 times higher than measured for KSTD1 (kcat/KmA = 4.71∙105 M-1 s-1). CONCLUSIONS We confirmed the existence of AcmB preference for a substrate with an undegraded isooctyl chain. However, we showed that KSTD1 which was reported to be inactive with such substrates can catalyze the reaction if the solubility problem is addressed.
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Affiliation(s)
- Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, 60115, Indonesia
- Laboratory of Proteomics, Research Center for Bio-Molecule Engineering (BIOME), Universitas Airlangga, Surabaya, 60115, Indonesia
- Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland.
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Glanowski M, Wójcik P, Procner M, Borowski T, Lupa D, Mielczarek P, Oszajca M, Świderek K, Moliner V, Bojarski AJ, Szaleniec M. Enzymatic Δ 1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Dawid Lupa
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Przemysław Mielczarek
- Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Department of Physical and Analytical Chemistry, Universitat Jaume I, 12071 Castellón, Spain
| | - Andrzej J. Bojarski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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Further Studies on the 3-Ketosteroid 9α-Hydroxylase of Rhodococcus ruber Chol-4, a Rieske Oxygenase of the Steroid Degradation Pathway. Microorganisms 2021; 9:microorganisms9061171. [PMID: 34072338 PMCID: PMC8228715 DOI: 10.3390/microorganisms9061171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
The biochemistry and genetics of the bacterial steroid catabolism have been extensively studied during the last years and their findings have been essential to the development of biotechnological applications. For instance, metabolic engineering of the steroid-eater strains has allowed to obtain intermediaries of industrial value. However, there are still some drawbacks that must be overcome, such as the redundancy of the steroid catabolism genes in the genome and a better knowledge of its genetic regulation. KshABs and KstDs are key enzymes involved in the aerobic breakage of the steroid nucleus. Rhodococcus ruber Chol-4 contains three kshAs genes, a single kshB gene and three kstDs genes within its genome. In the present work, the growth of R. ruber ΔkshA strains was evaluated on different steroids substrates; the promoter regions of these genes were analyzed; and their expression was followed by qRT-PCR in both wild type and ksh mutants. Additionally, the transcription level of the kstDs genes was studied in the ksh mutants. The results show that KshA2B and KshA1B are involved in AD metabolism, while KshA3B and KshA1B contribute to the cholesterol metabolism in R. ruber. In the kshA single mutants, expression of the remaining kshA and kstD genes is re-organized to survive on the steroid substrate. These data give insight into the fine regulation of steroid genes when several isoforms are present.
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Rohman A, Dijkstra BW. Application of microbial 3-ketosteroid Δ 1-dehydrogenases in biotechnology. Biotechnol Adv 2021; 49:107751. [PMID: 33823268 DOI: 10.1016/j.biotechadv.2021.107751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/27/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022]
Abstract
3-Ketosteroid Δ1-dehydrogenase catalyzes the 1(2)-dehydrogenation of 3-ketosteroid substrates using flavin adenine dinucleotide as a cofactor. The enzyme plays a crucial role in microbial steroid degradation, both under aerobic and anaerobic conditions, by initiating the opening of the steroid nucleus. Indeed, many microorganisms are known to possess one or more 3-ketosteroid Δ1-dehydrogenases. In the pharmaceutical industry, 3-ketosteroid Δ1-dehydrogenase activity is exploited to produce Δ1-3-ketosteroids, a class of steroids that display various biological activities. Many of them are used as active pharmaceutical ingredients in drug products, or as key precursors to produce pharmaceutically important steroids. Since 3-ketosteroid Δ1-dehydrogenase activity requires electron acceptors, among other considerations, Δ1-3-ketosteroid production has been industrially implemented using whole-cell fermentation with growing or metabolically active resting cells, in which the electron acceptors are available, rather than using the isolated enzyme. In this review we discuss biotechnological applications of microbial 3-ketosteroid Δ1-dehydrogenases, covering commonly used steroid-1(2)-dehydrogenating microorganisms, the bioprocess for preparing Δ1-3-ketosteroids, genetic engineering of 3-ketosteroid Δ1-dehydrogenases and related genes for constructing new, productive industrial strains, and microbial fermentation strategies for enhancing the product yield. Furthermore, we also highlight the recent development in the use of isolated 3-ketosteroid Δ1-dehydrogenases combined with a FAD cofactor regeneration system. Finally, in a somewhat different context, we summarize the role of 3-ketosteroid Δ1-dehydrogenase in cholesterol degradation by Mycobacterium tuberculosis and other mycobacteria. Because the enzyme is essential for the pathogenicity of these organisms, it may be a potential target for drug development to combat mycobacterial infections.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia; Laboratory of Proteomics, Research Center for Bio-Molecule Engineering (BIOME), Universitas Airlangga, Surabaya 60115, Indonesia; Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
| | - Bauke W Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
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Mao S, Chen Y, Sun J, Wei C, Song Z, Lu F, Qin HM. Enhancing the sustainability of KsdD as a biocatalyst for steroid transformation by immobilization on epoxy support. Enzyme Microb Technol 2021; 146:109777. [PMID: 33812565 DOI: 10.1016/j.enzmictec.2021.109777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 11/18/2022]
Abstract
The Δ1-dehydrogenation of 3-ketosteroid substrates is a crucial reaction in the production of steroids. Although 3-ketosteroid Δ1-dehydrogenase (KsdD) catalyzes this reaction with high efficiency and selectivity, the low stability and high cost of the purified enzyme catalyst have limited its industrial application. In this study, an epoxy support was used to evaluate the covalent immobilization of KsdD from Pimelobacter simplex, and the best androsta-1,4-diene-317-dione (ADD) production was achieved after optimized immobilization of KsdD enzyme in 1.5 M NaH2PO4- Na2HPO4 buffer (pH 6.5) for 12 h at 25 °C. The immobilized KsdD exhibited higher tolerance toward 20 % methanol. The dehydrogenation reaction reached a conversion efficiency of up to 90.0 % in 2 h when using 0.6 mg/mL of 4-androstene-317-dione (AD). The W299A and W299 G mutants of KsdD were also immobilized, and both showed the better catalytic performance with higher kcat/KM values compared with the wild type (WT). The immobilized W299A, W299 G and WT KsdD respectively maintained 70.5, 65.7 and 38.7 % of their initial activity at the end of 15 reaction cycles. Furthermore, the W299A retained 66.3 % of the initial activity after 30 days of incubation at 4 °C, and was more stable than free KsdD, Thus, the immobilized W299A is a promising biocatalyst for steroid dehydrogenation. In this study, we investigated the application of immobilized enzymes for the dehydrogenation of steroids, which will be of great importance for improving the development of green technology and sustainable use of biocatalysts in the steroid manufacturing industry.
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Affiliation(s)
- Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Ying Chen
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Jing Sun
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Cancan Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Zhan Song
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China.
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China.
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Shtratnikova VY, Sсhelkunov MI, Fokina VV, Bragin EY, Shutov AA, Donova MV. Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate. BMC Biotechnol 2021; 21:7. [PMID: 33441120 PMCID: PMC7807495 DOI: 10.1186/s12896-021-00668-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. RESULTS Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D. CONCLUSION The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.
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Affiliation(s)
- Victoria Yu Shtratnikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, h. 1, b. 40, Moscow, Russian Federation 119991
| | - Mikhail I. Sсhelkunov
- Skolkovo Institute of Science and Technology, Nobelya str., 3, Moscow, Russian Federation 121205
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow, Russian Federation 127994
| | - Victoria V. Fokina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
| | - Eugeny Y. Bragin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
| | - Andrey A. Shutov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
| | - Marina V. Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
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Girard J, Lanneau G, Delage L, Leroux C, Belcour A, Got J, Collén J, Boyen C, Siegel A, Dittami SM, Leblanc C, Markov GV. Semi-Quantitative Targeted Gas Chromatography-Mass Spectrometry Profiling Supports a Late Side-Chain Reductase Cycloartenol-to-Cholesterol Biosynthesis Pathway in Brown Algae. FRONTIERS IN PLANT SCIENCE 2021; 12:648426. [PMID: 33986764 PMCID: PMC8112355 DOI: 10.3389/fpls.2021.648426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 05/08/2023]
Abstract
Sterols are biologically important molecules that serve as membrane fluidity regulators and precursors of signaling molecules, either endogenous or involved in biotic interactions. There is currently no model of their biosynthesis pathways in brown algae. Here, we benefit from the availability of genome data and gas chromatography-mass spectrometry (GC-MS) sterol profiling using a database of internal standards to build such a model. We expand the set of identified sterols in 11 species of red, brown, and green macroalgae and integrate these new data with genomic data. Our analyses suggest that some metabolic reactions may be conserved despite the loss of canonical eukaryotic enzymes, like the sterol side-chain reductase (SSR). Our findings are consistent with the principle of metabolic pathway drift through enzymatic replacement and show that cholesterol synthesis from cycloartenol may be a widespread but variable pathway among chlorophyllian eukaryotes. Among the factors contributing to this variability, one could be the recruitment of cholesterol biosynthetic intermediates to make signaling molecules, such as the mozukulins. These compounds were found in some brown algae belonging to Ectocarpales, and we here provide a first mozukulin biosynthetic model. Our results demonstrate that integrative approaches can already be used to infer experimentally testable models, which will be useful to further investigate the biological roles of those newly identified algal pathways.
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Affiliation(s)
- Jean Girard
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Goulven Lanneau
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
- CNRS, Plateforme Corsaire-METABOMER (FR2424), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ludovic Delage
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Cédric Leroux
- CNRS, Plateforme Corsaire-METABOMER (FR2424), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Arnaud Belcour
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Jeanne Got
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Catherine Boyen
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Simon M. Dittami
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Catherine Leblanc
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Gabriel V. Markov
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
- *Correspondence: Gabriel V. Markov,
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Wojtkiewicz AM, Wójcik P, Procner M, Flejszar M, Oszajca M, Hochołowski M, Tataruch M, Mrugała B, Janeczko T, Szaleniec M. The efficient Δ 1-dehydrogenation of a wide spectrum of 3-ketosteroids in a broad pH range by 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans. J Steroid Biochem Mol Biol 2020; 202:105731. [PMID: 32777354 DOI: 10.1016/j.jsbmb.2020.105731] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022]
Abstract
Cholest-4-en-3-one Δ1-dehydrogenase (AcmB) from Sterolibacterium denitrificans, a key enzyme of the central degradation pathway of cholesterol, is a protein catalyzing Δ1-dehydrogenation of a wide range of 3-ketosteroids. In this study, we demonstrate the application of AcmB in the synthesis of 1-dehydro-3-ketosteroids and investigate the influence of reaction conditions on the catalytic performance of the enzyme. The recombinant AcmB expressed in E. coli BL21(DE3)Magic exhibits a broad pH optimum and pH stability in the range of 6.5 to 9.0. The activity-based pH optimum of AcmB reaction depends on the type of electron acceptor (2,6-dichloroindophenol - DCPIP, phenazine methosulfate - PMS or potassium hexacyanoferrate - K3[Fe(CN)6]) used in the biocatalytic process yielding the best kinetic properties for the reaction with a DCPIP/PMS mixture (kcat/Km = 1.4·105 s-1·M-1 at pH 9.0) followed by DCPIP (kcat/Km = 1.0·105 s-1·M-1 at pH = 6.5) and K3[Fe(CN)6] (kcat/Km = 0.5·102 s-1·M-1 at pH = 8.0). The unique feature of AcmB is its capability to convert both testosterone derivatives (C20-C22) as well as steroids substituted at C17 (C27-C30) such as cholest-4-en-3-one or (25R)-spirost-4-en-3-one (diosgenone). Apparent steady-state kinetic parameters were determined for both groups of AcmB substrates. In a batch reactor synthesis, the solubility of water-insoluble steroids was facilitated by the addition of a solubilizer, 2-hydroxypropyl-β-cyclodextrin, and organic co-solvent, 2-methoxyethanol. Catalytic properties characterization of AcmB was tested in fed-batch reactor set-ups, using 0.81 μM of isolated enzyme, PMS and aerobic atmosphere resulting in >99% conversion of the C17-C20 3-ketosteroids within 2 h. Finally, the whole cell E. coli system with recombinant enzyme was demonstrated as an efficient biocatalyst in the synthesis of 1-dehydro-3-ketosteroids.
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Affiliation(s)
- Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Monika Flejszar
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland; Department of Physical Chemistry, Faculty of Chemistry, Rzeszow University of Technology, Al. Powstańców Warszawy 6, PL35959 Rzeszów, Poland; Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL30387 Kraków, Poland
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL30387 Kraków, Poland
| | - Mateusz Hochołowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Tomasz Janeczko
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, PL50375 Wrocław, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland.
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Kollerov V, Shutov A, Kazantsev A, Donova M. Biotransformation of androstenedione and androstadienedione by selected Ascomycota and Zygomycota fungal strains. PHYTOCHEMISTRY 2020; 169:112160. [PMID: 31600654 DOI: 10.1016/j.phytochem.2019.112160] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/30/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Filamentous fungi is a huge phylum of lower eukaryotes with diverse activities towards various substrates, however, their biocatalytic potential towards steroids remains greatly underestimated. In this study, more than forty Ascomycota and Zygomycota fungal strains of 23 different genera were screened for the ability to catalyze structural modifications of 3-oxo-androstane steroids, - androst-4-ene-3,17-dione (AD) and androsta-1,4-diene-3,17-dione (ADD). Previously unexplored for these purposes strains of Absidia, Acremonium, Beauveria, Cunninghamella, Doratomyces, Drechslera, Fusarium, Gibberella genera were revealed capable of producing in a good yield valuable 7α-, 7β-, 11α- and 14α-hydroxylated derivatives, as well as 17β-reduced and 1(2)-dehydrogenated androstanes. The bioconversion routes of AD and ADD were proposed based on the key intermediates identification and time courses of the bioprocesses. Six ascomycete strains were discovered to provide effective 7β-hydroxylation of ADD which has not been so far reported. The structures of major products and intermediates were confirmed by HPLC, mass-spectrometry (MS), 1H and 13C NMR analyses. The results contribute to the knowledge on the functional diversity of steroid-transforming filamentous fungi. Previously unexplored fungal biocatalysts capable of effective performing structural modification of AD and ADD can be applied for industrial bioprocesses of new generation.
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Affiliation(s)
- Vyacheslav Kollerov
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290, Pushchino, Moscow Region, Russia; Pharmins Ltd., Institutskaya ul, 4, 142290, Pushchino, Moscow Region, Russia.
| | - Andrei Shutov
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290, Pushchino, Moscow Region, Russia; Pharmins Ltd., Institutskaya ul, 4, 142290, Pushchino, Moscow Region, Russia
| | - Alexey Kazantsev
- Moscow State University, GSP-1, Leninskiye Gori, 1, Chemical Department, Moscow, Russia
| | - Marina Donova
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290, Pushchino, Moscow Region, Russia; Pharmins Ltd., Institutskaya ul, 4, 142290, Pushchino, Moscow Region, Russia
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