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Wojtkiewicz AM, Oleksy G, Malinowska MA, Janeczko T. Enzymatic synthesis of a skin active ingredient - glochidone by 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans. J Steroid Biochem Mol Biol 2024; 241:106513. [PMID: 38521362 DOI: 10.1016/j.jsbmb.2024.106513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
In this study, we applied AcmB2, sourced from Sterolibacterium denitrificans, to catalyze the oxidative dehydrogenation of 3-ketolupeol (lupenone), a derivative of lupeol, triterpene obtained from birch bark. This enzymatic Δ1-dehydrogenation catalyzed by AcmB2 yielded glochidone, a bioactive compound frequently obtained from medicinal plants like Salvia trichoclada and Maytenus boria. Glochidone is known for its broad biological activities, including antibacterial, antifungal, anti-inflammatory, anticancer, antidiabetic as well as acetylcholinesterase inhibition. Our research demonstrates >99% conversion efficiency with 100% regioselectivity of the reaction. The effective conversion to glochidone employed an electron acceptor e.g., potassium hexacyanoferrate III, in mild, environmentally friendly conditions: 8-16% 2-hydroxypropyl-β-cyclodextrin, and 2-3% 2-methoxyethanol. AcmB2 reaction optimum was determined at pH 8.0 and 30 °C. Enzyme's biochemical attributes such as electron acceptor type, concentration and steroid substrate specificity were investigated. Among 4-, 5- and 6-ring steroid derivatives androst-4-en-3,17-dione and testosterone propionate were determined as the best substrates of AcmB2. Δ1-Dehydrogenation of substrates such as lupenone, diosgenone and 3-ketopetromyzonol was confirmed. We have assessed the antioxidant and rejuvenating characteristics of glochidone as an active component in formulations, considering its precursors, lupeol, and lupenone as well. Glochidone exhibited limited antioxidant and chelating capabilities compared to lupeol and reference compounds. However, it demonstrated robust rejuvenating properties, with a sirtuin induction level of 61.5 ± 1.87%, notably surpassing that of the reference substance, E-resveratrol (45.15 ± 0.09%). Additionally, glochidone displayed 26.5±0.67 and 19.41±0.76% inhibition of elastase and collagenase, respectively. The safety of all studied triterpenes was confirmed on skin reconstructed human Epidermis model. These findings provide valuable insights into the potential applications of glochidone in formulations aimed at addressing skin health concerns. This research presents the first example of an enzyme in the 3-ketosteroid dehydrogenase (KstD) family catalyzing the Δ1-dehydrogenation of a pentacyclic triterpene. We also explored structural differences between AcmB, AcmB2, and related KstDs pointing to G52 and P532 as potentially responsible for the unique substrate specificity of AcmB2. Our findings not only highlight the enzyme's capabilities but also present novel enzymatic pathways for bioactive compound synthesis.
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Affiliation(s)
- Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow PL30239, Poland.
| | - Gabriela Oleksy
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow PL30239, Poland
| | - Magdalena A Malinowska
- Organic Chemistry and Technology Department, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawa 24, Krakow 31-155, Poland
| | - Tomasz Janeczko
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, Wrocław 50-375, Poland
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Yang T, Li G, Xu Y, He X, Song B, Cao Y. Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia. BMC Microbiol 2024; 24:169. [PMID: 38760705 PMCID: PMC11100065 DOI: 10.1186/s12866-024-03329-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) is an endocrinopathy in childbearing-age females which can cause many complications, such as diabetes, obesity, and dyslipidemia. The metabolic disorders in patients with PCOS were linked to gut microbial dysbiosis. However, the correlation between the gut microbial community and dyslipidemia in PCOS remains unillustrated. Our study elucidated the different gut microbiota in patients with PCOS and dyslipidemia (PCOS.D) compared to those with only PCOS and healthy women. RESULTS In total, 18 patients with PCOS, 16 healthy females, and 18 patients with PCOS.D were enrolled. The 16 S rRNA sequencing in V3-V4 region was utilized for identifying the gut microbiota, which analyzes species annotation, community diversity, and community functions. Our results showed that the β diversity of gut microbiota did not differ significantly among the three groups. Regarding gut microbiota dysbiosis, patients with PCOS showed a decreased abundance of Proteobacteria, and patients with PCOS.D showed an increased abundance of Bacteroidota compared to other groups. With respect to the gut microbial imbalance at genus level, the PCOS.D group showed a higher abundance of Clostridium_sensu_stricto_1 compared to other two groups. Furthermore, the abundances of Faecalibacterium and Holdemanella were lower in the PCOS.D than those in the PCOS group. Several genera, including Faecalibacterium and Holdemanella, were negatively correlated with the lipid profiles. Pseudomonas was negatively correlated with luteinizing hormone levels. Using PICRUSt analysis, the gut microbiota community functions suggested that certain metabolic pathways (e.g., amino acids, glycolysis, and lipid) were altered in PCOS.D patients as compared to those in PCOS patients. CONCLUSIONS The gut microbiota characterizations in patients with PCOS.D differ from those in patients with PCOS and controls, and those might also be related to clinical parameters. This may have the potential to become an alternative therapy to regulate the clinical lipid levels of patients with PCOS in the future.
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Affiliation(s)
- Tianjin Yang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Guanjian Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, China
- Ministry of Education Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, China
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, 230032, China
- Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, 230032, China
| | - Yuping Xu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, China
- Ministry of Education Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, China
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, 230032, China
- Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, 230032, China
| | - Xiaojin He
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, China.
- Reproductive Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Bing Song
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, China.
- Ministry of Education Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, China.
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, 230032, China.
- Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, 230032, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, China.
- Ministry of Education Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, China.
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, 230032, China.
- Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, 230032, China.
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Roth AT, Philips JA, Chandra P. The role of cholesterol and its oxidation products in tuberculosis pathogenesis. IMMUNOMETABOLISM (COBHAM, SURREY) 2024; 6:e00042. [PMID: 38693938 PMCID: PMC11060060 DOI: 10.1097/in9.0000000000000042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
Mycobacterium tuberculosis causes tuberculosis (TB), one of the world's most deadly infections. Lipids play an important role in M. tuberculosis pathogenesis. M. tuberculosis grows intracellularly within lipid-laden macrophages and extracellularly within the cholesterol-rich caseum of necrotic granulomas and pulmonary cavities. Evolved from soil saprophytes that are able to metabolize cholesterol from organic matter in the environment, M. tuberculosis inherited an extensive and highly conserved machinery to metabolize cholesterol. M. tuberculosis uses this machinery to degrade host cholesterol; the products of cholesterol degradation are incorporated into central carbon metabolism and used to generate cell envelope lipids, which play important roles in virulence. The host also modifies cholesterol by enzymatically oxidizing it to a variety of derivatives, collectively called oxysterols, which modulate cholesterol homeostasis and the immune response. Recently, we found that M. tuberculosis converts host cholesterol to an oxidized metabolite, cholestenone, that accumulates in the lungs of individuals with TB. M. tuberculosis encodes cholesterol-modifying enzymes, including a hydroxysteroid dehydrogenase, a putative cholesterol oxidase, and numerous cytochrome P450 monooxygenases. Here, we review what is known about cholesterol and its oxidation products in the pathogenesis of TB. We consider the possibility that the biological function of cholesterol metabolism by M. tuberculosis extends beyond a nutritional role.
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Affiliation(s)
- Andrew T. Roth
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer A. Philips
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Pallavi Chandra
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, Watanabe T, Fukui M, Hanada S, Tank M, Neufeld JD. Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 2024; 627:915-922. [PMID: 38480893 PMCID: PMC10972752 DOI: 10.1038/s41586-024-07180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/08/2024] [Indexed: 04/01/2024]
Abstract
Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, Waterloo, Ontario, Canada.
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.
| | - N A Shaw
- University of Waterloo, Waterloo, Ontario, Canada
| | - S Nagashima
- Tokyo Metropolitan University, Tokyo, Japan
- Kanagawa University, Yokohama, Japan
| | - J J Venkiteswaran
- University of Waterloo, Waterloo, Ontario, Canada
- Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - S L Schiff
- University of Waterloo, Waterloo, Ontario, Canada
| | - T Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - M Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - S Hanada
- Tokyo Metropolitan University, Tokyo, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Tank
- Tokyo Metropolitan University, Tokyo, Japan
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - J D Neufeld
- University of Waterloo, Waterloo, Ontario, Canada.
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5
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Zhang X, He X, Pan D, Shi L, Wu Y, Yang Y, Zhu Y, Wang Y, Wang H, Pu L, He S, Meng L, Li J. Effects of thermal exposure to disposable plastic tableware on human gut microbiota and metabolites: A quasi-experimental study. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132800. [PMID: 37866144 DOI: 10.1016/j.jhazmat.2023.132800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
The aim of this quasi-experimental study was to determine the alterations in gut microbiota and metabolism in humans who consume hot food served in disposable plastic tableware (DPT). Participants in the exposure and control groups were provided three hot meals in DPT (n = 30) or non-DPT (n = 30), respectively. After a month of observation, individuals in the exposure group discontinued the three meals provided in DPT (n = 27) for 1 month as the post-exposure group. Fecal samples were collected and tested for microplastics (MPs) detection using LDIR and gut microbiota identification based on the 16 S rRNA. Urine samples were used for metabolite analysis using LC-MS/MS. Results showed that the level of MPs in feces was lower in the post-exposure group compared with the exposure group. Furthermore, the abundance of the phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidota in the exposure and post-exposure groups were significantly different compared with the control group. Changes in microbiota abundance and metabolite levels were mainly associated with central nervous system effects, energy metabolism, and inflammation, suggesting that thermal exposure to DPT for 1 month has considerable health effects.
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Affiliation(s)
- Xue Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Xiaoxue He
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Degong Pan
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Liping Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Yueping Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Yue Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Yongbin Zhu
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Yanrong Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Huihui Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Lining Pu
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Shulan He
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China.
| | - Lingchen Meng
- Department of Sanitary Chemistry, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China.
| | - Jiangping Li
- Department of Epidemiology and Health Statistics, School of Public Health, Ningxia Medical University, Yinchuan, Ningxia 750004, China; Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, Yinchuan, Ningxia 750004, China.
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Brown KL, Krekhno JMC, Xing S, Huan T, Eltis LD. Cholesterol-Mediated Coenzyme A Depletion in Catabolic Mutants of Mycobacteria Leads to Toxicity. ACS Infect Dis 2024; 10:107-119. [PMID: 38054469 DOI: 10.1021/acsinfecdis.3c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Cholesterol is a critical growth substrate for Mycobacterium tuberculosis (Mtb) during infection, and the cholesterol catabolic pathway has been targeted for the development of new antimycobacterial agents. A key metabolite in cholesterol catabolism is 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP). Many of the HIP metabolites are acyl-coenzyme A (CoA) thioesters, whose accumulation in deletion mutants can cause cholesterol-mediated toxicity. We used LC-MS/MS analysis to demonstrate that deletion of genes involved in HIP catabolism leads to acyl-CoA accumulation with concomitant depletion of free CoASH, leading to dysregulation of central metabolic pathways. CoASH and acyl-CoAs inhibited PanK, the enzyme that catalyzes the first step in the transformation of pantothenate to CoASH. Inhibition was competitive with respect to ATP with Kic values ranging from 9 μM for CoASH to 57 μM for small acyl-CoAs and 180 ± 30 μM for cholesterol-derived acyl-CoA. These findings link two critical metabolic pathways and suggest that therapeutics targeting cholesterol catabolic enzymes could both prevent the utilization of an important growth substrate and simultaneously sequester CoA from essential cellular processes, leading to bacterial toxicity.
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Affiliation(s)
- Kirstin L Brown
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Jessica M C Krekhno
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Shipei Xing
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Tao Huan
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
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7
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Wu E, Wang K, Liu Z, Wang J, Yan H, Zhu X, Zhu X, Chen B. Metabolic and Microbial Profiling of Soil Microbial Community under Per- and Polyfluoroalkyl Substance (PFAS) Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21855-21865. [PMID: 38086098 DOI: 10.1021/acs.est.3c07020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) represent significant stress to organisms and are known to disrupt microbial community structure and function. Nevertheless, a detailed knowledge of the soil microbial community responding to PFAS stress at the metabolism level is required. Here we integrated UPLC-HRMS-based metabolomics data with 16S rRNA and ITS amplicon data across soil samples collected adjacent to a fluoropolymer production facility to directly identify the biochemical intermediates in microbial metabolic pathways and the interactions with microbial community structure under PFAS stress. A strong correlation between metabolite and microbial diversity was observed, which demonstrated significant variations in soil metabolite profiles and microbial community structures along with the sampling locations relative to the facility. Certain key metabolites were identified in the metabolite-PFAS co-occurrence network, functioning on microbial metabolisms including lipid metabolism, amino acid metabolism, and secondary metabolite biosynthesis. These results provide novel insights into the impacts of PFAS contamination on soil metabolomes and microbiomes. We suggest that soil metabolomics is an informative and useful tool that could be applied to reinforce the chemical evidence on the disruption of microbial ecological traits.
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Affiliation(s)
- Enhui Wu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Kun Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhengzheng Liu
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, People's Republic of China
| | - Jing Wang
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, People's Republic of China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xiaomin Zhu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Innovation Center of Yangtze River Delta, Zhejiang University, Haining, Zhejiang 311400, People's Republic of China
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8
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Kannan P, Verma I, Banerjee B, Saleena LM. Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach. Arch Microbiol 2023; 206:27. [PMID: 38112856 DOI: 10.1007/s00203-023-03765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.
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Affiliation(s)
- Priya Kannan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Ishita Verma
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Bhargabi Banerjee
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India.
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Liu X, Zhang J, Yuan C, Du G, Han S, Shi J, Sun J, Zhang B. Improving the production of 9α-hydroxy-4-androstene-3,17-dione from phytosterols by 3-ketosteroid-Δ 1-dehydrogenase deletions and multiple genetic modifications in Mycobacterium fortuitum. Microb Cell Fact 2023; 22:53. [PMID: 36922830 PMCID: PMC10018825 DOI: 10.1186/s12934-023-02052-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND 9α-hydroxyandrost-4-ene-3,17-dione (9-OHAD) is a significant intermediate for the synthesis of glucocorticoid drugs. However, in the process of phytosterol biotransformation to manufacture 9-OHAD, product degradation, and by-products restrict 9-OHAD output. In this study, to construct a stable and high-yield 9-OHAD producer, we investigated a combined strategy of blocking Δ1‑dehydrogenation and regulating metabolic flux. RESULTS Five 3-Ketosteroid-Δ1-dehydrogenases (KstD) were identified in Mycobacterium fortuitum ATCC 35855. KstD2 showed the highest catalytic activity on 3-ketosteroids, followed by KstD3, KstD1, KstD4, and KstD5, respectively. In particular, KstD2 had a much higher catalytic activity for C9 hydroxylated steroids than for C9 non-hydroxylated steroids, whereas KstD3 showed the opposite characteristics. The deletion of kstDs indicated that KstD2 and KstD3 were the main causes of 9-OHAD degradation. Compared with the wild type M. fortuitum ATCC 35855, MFΔkstD, the five kstDs deficient strain, realized stable accumulation of 9-OHAD, and its yield increased by 42.57%. The knockout of opccr or the overexpression of hsd4A alone could not reduce the metabolic flux of the C22 pathway, while the overexpression of hsd4A based on the knockout of opccr in MFΔkstD could remarkably reduce the contents of 9,21 ‑dihydroxy‑20‑methyl‑pregna‑4‑en‑3‑one (9-OHHP) by-products. The inactivation of FadE28-29 leads to a large accumulation of incomplete side-chain degradation products. Therefore, hsd4A and fadE28-29 were co-expressed in MFΔkstDΔopccr successfully eliminating the two by-products. Compared with MFΔkstD, the purity of 9-OHAD improved from 80.24 to 90.14%. Ultimately, 9‑OHAD production reached 12.21 g/L (83.74% molar yield) and the productivity of 9-OHAD was 0.0927 g/L/h from 20 g/L phytosterol. CONCLUSIONS KstD2 and KstD3 are the main dehydrogenases that lead to 9-OHAD degradation. Hsd4A and Opccr are key enzymes regulating the metabolic flux of the C19- and C22-pathways. Overexpression of fadE28-29 can reduce the accumulation of incomplete degradation products of the side chains. According to the above findings, the MF-FA5020 transformant was successfully constructed to rapidly and stably accumulate 9-OHAD from phytosterols. These results contribute to the understanding of the diversity and complexity of steroid catabolism regulation in actinobacteria and provide a theoretical basis for further optimizing industrial microbial catalysts.
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Affiliation(s)
- Xiangcen Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingxian Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenyang Yuan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Guilin Du
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Suwan Han
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Junsong Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Baoguo Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.
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10
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Jiang X, Xue Z, Chen W, Xu M, Liu H, Liang J, Zhang L, Sun Y, Liu C, Yang X. Biotransformation kinetics and pathways of typical synthetic progestins in soil microcosms. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130684. [PMID: 36586332 DOI: 10.1016/j.jhazmat.2022.130684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Gestodene (GES), altrenogest (ALT), and medroxyprogesterone acetate (MPA) are three potent synthetic progestins detected in agricultural soils; however, their biotransformation outcomes in soils remain unclear. This study explored the biotransformation of these progestins in five agricultural soils with different physicochemical properties. The biotransformation data were well-described by a first-order decay model (R2 = 0.83-0.99), with estimated half-lives ranging between 12.1 and 188 h. Amplicon sequencing indicated that the presence of progestins changed the bacterial richness and community structure in the soils. Linear correlation, canonical correlation, and two-way correlation network analysis revealed that soil properties can affect biotransformation rates by interfering with progestin-soil interactions or with keystone taxa in soils. The clustermap demonstrated the formation of abundant transformation products (TPs). Isomerization and C4(5) hydrogenation were the major transformation pathways for GES (yields of ∼ 13.7 % and ∼ 10.6 %, respectively). Aromatic dehydrogenation was the major transformation pathway for ALT (yield of ∼ 17.4 %). The C17 hydrolysis with subsequent dehydration and hydrogenation was the major transformation pathway for MPA (yield of ∼ 196 %). In particular, some TPs exhibited progestagenic, androgenic, or estrogenic activity. This study highlights the importance of evaluating the ecotoxicity of progestin and TP mixtures for better understanding their risks in the environment.
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Affiliation(s)
- Xiuping Jiang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhongye Xue
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Weisong Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Manxin Xu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - He Liu
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510655, PR China
| | - Jiahao Liang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510655, PR China
| | - Lu Zhang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yan Sun
- Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, Guangdong 510650, PR China
| | - Churong Liu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
| | - Xingjian Yang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
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11
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Begley LA, Opron K, Bian G, Kozik AJ, Liu C, Felton J, Wen B, Sun D, Huang YJ. Effects of Fluticasone Propionate on Klebsiella pneumoniae and Gram-Negative Bacteria Associated with Chronic Airway Disease. mSphere 2022; 7:e0037722. [PMID: 36342141 PMCID: PMC9769713 DOI: 10.1128/msphere.00377-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Inhaled corticosteroids (ICS) are commonly prescribed first-line treatments for asthma and chronic obstructive pulmonary disease (COPD). Recent evidence has shown that ICS use is associated with changes in the airway microbiome, which may impact clinical outcomes such as potential increased risk for pneumonia in COPD. Although the immunomodulatory effects of corticosteroids are well appreciated, whether ICS could directly influence the behavior of respiratory tract bacteria has been unknown. In this pilot study we explored the effects of fluticasone proprionate, a commonly prescribed inhaled corticosteroid, on respiratory bacteria with an expanded focus on Klebsiella pneumoniae, a species previously implicated in fluticasone-associated pneumonia in COPD. We observed significant effects of fluticasone proprionate on growth responses of K. pneumoniae, as well as other bacterial species isolated from asthmatic patients. Fluticasone-exposed K. pneumoniae displayed altered expression of several bacterial genes and reduced the metabolic activity of bronchial epithelial cells and their expression of human β-defensin 2. Targeted assays identified a fluticasone metabolite from fluticasone-exposed K. pneumoniae cells, suggesting this species may be capable of metabolizing fluticasone proprionate. Collectively, these observations support the hypothesis that specific members of the airway microbiota possess the functional repertoire to respond to or potentially utilize corticosteroids in their microenvironment. These findings lay a foundation for novel research directions into the potential direct effects of ICS, often prescribed long term to patients, on the broader airway microbial community and on the behavior of specific microbial species implicated in asthma and COPD outcomes. IMPORTANCE Inhaled corticosteroids are widely prescribed for many respiratory diseases, including asthma and COPD. While they benefit many patients, corticosteroids can also have negative effects. Some patients do not improve with treatment and even experience adverse side effects. Recent studies have shown that inhaled corticosteroids can change the make-up of bacteria in the human respiratory tract. However, whether these medications can directly impact the behavior of such bacteria has been unknown. Here, we explored the effects of fluticasone propionate, a commonly prescribed inhaled corticosteroid, on Klebsiella pneumoniae and other airway bacteria of interest, including primary species isolated from adult asthma patients. We provide evidence of growth responses to direct fluticasone exposure in culture and further examined fluticasone's effects on K. pneumoniae, including gene expression changes and effects of fluticasone-exposed bacteria on airway cells. These findings indicate that members of the human airway bacterial community possess the functional ability to respond to corticosteroids, which may have implications for the heterogeneity of treatment response observed clinically.
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Affiliation(s)
- Lesa A. Begley
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristopher Opron
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Guowu Bian
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ariangela J. Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Cai Liu
- Pharmacokinetics and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeremy Felton
- Pharmacokinetics and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Bo Wen
- Pharmacokinetics and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Duxin Sun
- Pharmacokinetics and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Yvonne J. Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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12
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Lobastova T, Fokina V, Pozdnyakova-Filatova I, Tarlachkov S, Shutov A, Donova M. Insight into Different Stages of Steroid Degradation in Thermophilic Saccharopolyspora hirsuta VKM Ac-666 T Strain. Int J Mol Sci 2022; 23:ijms232416174. [PMID: 36555813 PMCID: PMC9782250 DOI: 10.3390/ijms232416174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Steroids are abundant molecules in nature, and various microorganisms evolved to utilize steroids. Thermophilic actinobacteria play an important role in such processes. However, very few thermophiles have so far been reported capable of degrading or modifying natural sterols. Recently, genes putatively involved in the sterol catabolic pathway have been revealed in the moderately thermophilic actinobacterium Saccharopolyspora hirsuta VKM Ac-666T, but peculiarities of strain activity toward sterols are still poorly understood. S. hirsuta catalyzed cholesterol bioconversion at a rate significantly inferior to that observed for mesophilic actinobacteria (mycobacteria and rhodococci). Several genes related to different stages of steroid catabolism increased their expression in response to cholesterol as was shown by transcriptomic studies and verified by RT-qPCR. Sequential activation of genes related to the initial step of cholesterol side chain oxidation (cyp125) and later steps of steroid core degradation (kstD3, kshA, ipdF, and fadE30) was demonstrated for the first time. The activation correlates with a low cholesterol conversion rate and intermediate accumulation by the strain. The transcriptomic analyses revealed that the genes involved in sterol catabolism are linked functionally, but not transcriptionally. The results contribute to the knowledge on steroid catabolism in thermophilic actinobacteria and could be used at the engineering of microbial catalysts.
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Affiliation(s)
- Tatyana Lobastova
- Laboratory of Bioengineering of Microbial Producers, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
| | - Victoria Fokina
- Laboratory of Bioengineering of Microbial Producers, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
| | - Irina Pozdnyakova-Filatova
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
| | - Sergey Tarlachkov
- Laboratory of Bioengineering of Microbial Producers, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
| | - Andrey Shutov
- Laboratory of Bioengineering of Microbial Producers, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
| | - Marina Donova
- Laboratory of Bioengineering of Microbial Producers, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
- Correspondence:
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13
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Weckerle T, Ewald H, Guth P, Knorr K, Philipp B, Holert J. Biogas digestate as a sustainable phytosterol source for biotechnological cascade valorization. Microb Biotechnol 2022; 16:337-349. [PMID: 36415958 PMCID: PMC9871531 DOI: 10.1111/1751-7915.14174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/24/2022] Open
Abstract
Every year, several million tonnes of anaerobic digestate are produced worldwide as a by-product of the biogas industry, most of which is applied as agricultural fertilizer. However, in the context of a circular bioeconomy, more sustainable uses of residual digestate biomass would be desirable. This study investigates the fate of the sterol lipids β-sitosterol and cholesterol from the feedstocks to the final digestates of three agricultural and one biowaste biogas plants to assess if sterols are degraded during anaerobic digestion or if they remain in the digestate, which could provide a novel opportunity for digestate cascade valorization. Gas chromatographic analyses showed that feedstock sterols were not degraded during anaerobic digestion, resulting in their accumulation in the digestates to up to 0.15% of the dry weight. The highest concentrations of around 1440 mg β-sitosterol and 185 mg cholesterol per kg dry weight were found in liquid digestate fractions, suggesting partial sterol solubilization. Methanogenic batch cultures spiked with β-sitosterol, cholesterol, testosterone and β-oestradiol confirmed that steroids persist during anaerobic digestion. Mycobacterium neoaurum was able to transform digestate sterols quantitatively into androstadienedione, a platform chemical for steroid hormones, without prior sterol extraction or purification. These results suggest that digestate from agricultural and municipal biowaste is an untapped resource for natural sterols for biotechnological applications, providing a new strategy for digestate cascade valorization beyond land application.
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Affiliation(s)
- Tim Weckerle
- Institute for Molecular Microbiology and BiotechnologyMicrobial Biotechnology & Ecology Group, University of MünsterMünsterGermany
| | - Helen Ewald
- Institute for Molecular Microbiology and BiotechnologyMicrobial Biotechnology & Ecology Group, University of MünsterMünsterGermany
| | - Patrick Guth
- Institute of Landscape Ecology, Ecohydrology & Biogeochemistry GroupUniversity of MünsterMünsterGermany
| | - Klaus‐Holger Knorr
- Institute of Landscape Ecology, Ecohydrology & Biogeochemistry GroupUniversity of MünsterMünsterGermany
| | - Bodo Philipp
- Institute for Molecular Microbiology and BiotechnologyMicrobial Biotechnology & Ecology Group, University of MünsterMünsterGermany
| | - Johannes Holert
- Institute for Molecular Microbiology and BiotechnologyMicrobial Biotechnology & Ecology Group, University of MünsterMünsterGermany
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14
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Sugden S, Holert J, Cardenas E, Mohn WW, Stein LY. Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges. THE ISME JOURNAL 2022; 16:2503-2512. [PMID: 35906397 PMCID: PMC9562138 DOI: 10.1038/s41396-022-01296-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.
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Affiliation(s)
- Scott Sugden
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada.
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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15
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Bacterial Hydratases Involved in Steroid Side Chain Degradation Have Distinct Substrate Specificities. J Bacteriol 2022; 204:e0023622. [PMID: 36000836 PMCID: PMC9491828 DOI: 10.1128/jb.00236-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actinobacterial MaoC family enoyl coenzyme A (CoA) hydratases catalyze the addition of water across the double bond of CoA esters during steroid side chain catabolism. We determined that heteromeric MaoC type hydratases, exemplified by ChsH1-ChsH2Mtb of Mycobacterium tuberculosis and CasM-CasORjost from Rhodococcus jostii RHA1, are specific toward a 3-carbon side chain steroid metabolite, consistent with their roles in the last β-oxidation cycle of steroid side chain degradation. Hydratases containing two fused MaoC domains are responsible for the degradation of longer steroid side chains. These hydratases, encoded in the cholesterol degradation gene clusters of M. tuberculosis and R. jostii RHA1, have broad specificity and were able to catalyze the hydration of the 5-carbon side chain of both cholesterol and bile acid metabolites. Surprisingly, the homologous hydratases from the bile acid degradation pathway have low catalytic efficiencies or no activity toward the 5-carbon side chain bile acid metabolites, cholyl-enoyl-CoA, lithocholyl-enoyl-CoA, and chenodeoxycholyl-enoyl-CoA. Instead, these hydratases preferred a cholate metabolite with oxidized steroid rings and a planar ring structure. Together, the results suggest that ring oxidation occurs prior to side chain degradation in the actinobacterial bile acid degradation pathway. IMPORTANCE Characterization of the substrate specificity of hydratases described here will facilitate the development of specific inhibitors that may be useful as novel therapeutics against M. tuberculosis and to metabolically engineer bacteria to produce steroid pharmaceuticals with desired steroid rings and side chain structures.
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16
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Malinga NA, Nzuza N, Padayachee T, Syed PR, Karpoormath R, Gront D, Nelson DR, Syed K. An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species. Microorganisms 2022; 10:microorganisms10050871. [PMID: 35630316 PMCID: PMC9143469 DOI: 10.3390/microorganisms10050871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 01/04/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are heme thiolate proteins present in species across the biological kingdoms. By virtue of their broad substrate promiscuity and regio- and stereo-selectivity, these enzymes enhance or attribute diversity to secondary metabolites. Actinomycetes species are well-known producers of secondary metabolites, especially Salinispora species. Despite the importance of P450s, a comprehensive comparative analysis of P450s and their role in secondary metabolism in Salinispora species is not reported. We therefore analyzed P450s in 126 strains from three different species Salinispora arenicola, S. pacifica, and S. tropica. The study revealed the presence of 2643 P450s that can be grouped into 45 families and 103 subfamilies. CYP107 and CYP125 families are conserved, and CYP105 and CYP107 families are bloomed (a P450 family with many members) across Salinispora species. Analysis of P450s that are part of secondary metabolite biosynthetic gene clusters (smBGCs) revealed Salinispora species have an unprecedented number of P450s (1236 P450s-47%) part of smBGCs compared to other bacterial species belonging to the genera Streptomyces (23%) and Mycobacterium (11%), phyla Cyanobacteria (8%) and Firmicutes (18%) and the classes Alphaproteobacteria (2%) and Gammaproteobacteria (18%). A peculiar characteristic of up to six P450s in smBGCs was observed in Salinispora species. Future characterization Salinispora species P450s and their smBGCs have the potential for discovering novel secondary metabolites.
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Affiliation(s)
- Nsikelelo Allison Malinga
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
| | - Puleng Rosinah Syed
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (P.R.S.); (R.K.)
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (P.R.S.); (R.K.)
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.); Tel.: +19-014-488-303 (D.R.N.); +27-035-902-6857 (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
- Correspondence: (D.R.N.); (K.S.); Tel.: +19-014-488-303 (D.R.N.); +27-035-902-6857 (K.S.)
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17
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Steroid Metabolism in Thermophilic Actinobacterium Saccharopolyspora hirsuta VKM Ac-666 T. Microorganisms 2021; 9:microorganisms9122554. [PMID: 34946155 PMCID: PMC8708139 DOI: 10.3390/microorganisms9122554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 12/03/2022] Open
Abstract
The application of thermophilic microorganisms opens new prospects in steroid biotechnology, but little is known to date on steroid catabolism by thermophilic strains. The thermophilic strain Saccharopolyspora hirsuta VKM Ac-666T has been shown to convert various steroids and to fully degrade cholesterol. Cholest-4-en-3-one, cholesta-1,4-dien-3-one, 26-hydroxycholest-4-en-3-one, 3-oxo-cholest-4-en-26-oic acid, 3-oxo-cholesta-1,4-dien-26-oic acid, 26-hydroxycholesterol, 3β-hydroxy-cholest-5-en-26-oic acid were identified as intermediates in cholesterol oxidation. The structures were confirmed by 1H and 13C-NMR analyses. Aliphatic side chain hydroxylation at C26 and the A-ring modification at C3, which are putatively catalyzed by cytochrome P450 monooxygenase CYP125 and cholesterol oxidase, respectively, occur simultaneously in the strain and are followed by cascade reactions of aliphatic sidechain degradation and steroid core destruction via the known 9(10)-seco-pathway. The genes putatively related to the sterol and bile acid degradation pathways form three major clusters in the S. hirsuta genome. The sets of the genes include the orthologs of those involved in steroid catabolism in Mycobacterium tuberculosis H37Rv and Rhodococcus jostii RHA1 and related actinobacteria. Bioinformatics analysis of 52 publicly available genomes of thermophilic bacteria revealed only seven candidate strains that possess the key genes related to the 9(10)-seco pathway of steroid degradation, thus demonstrating that the ability to degrade steroids is not widespread among thermophilic bacteria.
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18
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Feller FM, Eilebrecht S, Nedielkov R, Yücel O, Alvincz J, Salinas G, Ludwig KC, Möller H, Philipp B. Investigations on the Degradation of the Bile Salt Cholate via the 9,10- Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain Chol11. Microorganisms 2021; 9:microorganisms9102146. [PMID: 34683472 PMCID: PMC8540908 DOI: 10.3390/microorganisms9102146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/30/2023] Open
Abstract
Bile salts such as cholate are steroid compounds from the digestive tracts of vertebrates, which enter the environment upon excretion, e.g., in manure. Environmental bacteria degrade bile salts aerobically via two pathway variants involving intermediates with Δ1,4- or Δ4,6-3-keto-structures of the steroid skeleton. Recent studies indicated that degradation of bile salts via Δ4,6-3-keto intermediates in Sphingobium sp. strain Chol11 proceeds via 9,10-seco cleavage of the steroid skeleton. For further elucidation, the presumptive product of this cleavage, 3,12β-dihydroxy-9,10-seco-androsta-1,3,5(10),6-tetraene-9,17-dione (DHSATD), was provided to strain Chol11 in a co-culture approach with Pseudomonas stutzeri Chol1 and as purified substrate. Strain Chol11 converted DHSATD to the so far unknown compound 4-methyl-3-deoxy-1,9,12-trihydroxyestra-1,3,5(10)7-tetraene-6,17-dione (MDTETD), presumably in a side reaction involving an unusual ring closure. MDTETD was neither degraded by strains Chol1 and Chol11 nor in enrichment cultures. Functional transcriptome profiling of zebrafish embryos after exposure to MDTETD identified a significant overrepresentation of genes linked to hormone responses. In both pathway variants, steroid degradation intermediates transiently accumulate in supernatants of laboratory cultures. Soil slurry experiments indicated that bacteria using both pathway variants were active and also released their respective intermediates into the environment. This instance could enable the formation of recalcitrant steroid metabolites by interspecies cross-feeding in agricultural soils.
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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.); (O.Y.); (K.C.L.)
| | - Sebastian Eilebrecht
- Fraunhofer Attract Eco’n’OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany; (S.E.); (J.A.)
| | - Ruslan Nedielkov
- Institute for Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (R.N.); (H.M.)
| | - Onur Yücel
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
| | - Julia Alvincz
- Fraunhofer Attract Eco’n’OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany; (S.E.); (J.A.)
| | - Gabriela Salinas
- NGS-Services for Integrative Genomics, Institute for Human Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Kevin Christopher Ludwig
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
| | - Heiko Möller
- Institute for Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (R.N.); (H.M.)
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
- Department for Environmental Microbiology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany
- Correspondence: ; Tel.: +49-251-8339827; Fax: +49-251-8338388
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19
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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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20
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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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21
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Harthern-Flint SL, Dolfing J, Mrozik W, Meynet P, Eland LE, Sim M, Davenport RJ. Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557. Front Microbiol 2021; 12:670928. [PMID: 34276604 PMCID: PMC8281962 DOI: 10.3389/fmicb.2021.670928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.
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Affiliation(s)
| | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.,Faculty Engineering and Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wojciech Mrozik
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Paola Meynet
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Sim
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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22
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Mainetti T, Palmisano M, Rezzonico F, Stres B, Kern S, Smits THM. Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge. Arch Microbiol 2021; 203:4209-4219. [PMID: 34080042 PMCID: PMC8360860 DOI: 10.1007/s00203-021-02409-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 10/31/2022]
Abstract
Conjugated estrogens, such as 17β-estradiol-3-sulfate (E2-3S), can be released into aquatic environments through wastewater treatment plants (WWTP). There, they are microbiologically degraded into free estrogens, which can have harmful effects on aquatic wildlife. Here, the degradation of E2-3S in environmental samples taken upstream, downstream and at the effluent of a WWTP was assessed. Sediment and biofilm samples were enriched for E2-3S-degrading microorganisms, yielding a broad diversity of bacterial isolates, including known and novel degraders of estrogens. Since E2-3S-degrading bacteria were also isolated in the sample upstream of the WWTP, the WWTP does not influence the ability of the microbial community to degrade E2-3S.
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Affiliation(s)
- Tamara Mainetti
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Marilena Palmisano
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Blaž Stres
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia.,Jozef Stefan Institute, Ljubljana, Slovenia
| | - Susanne Kern
- Environmental Analytics Group, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.
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23
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Hsiao T, Chen Y, Meng M, Chuang M, Horinouchi M, Hayashi T, Wang P, Chiang Y. Mechanistic and phylogenetic insights into actinobacteria-mediated oestrogen biodegradation in urban estuarine sediments. Microb Biotechnol 2021; 14:1212-1227. [PMID: 33764689 PMCID: PMC8085986 DOI: 10.1111/1751-7915.13798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/24/2021] [Accepted: 02/28/2021] [Indexed: 12/01/2022] Open
Abstract
Steroidal oestrogens are often accumulated in urban estuarine sediments worldwide at microgram per gram levels. These aromatic steroids have been classified as endocrine disruptors and group 1 carcinogens. Microbial degradation is a naturally occurring mechanism that mineralizes oestrogens in the biosphere; however, the corresponding genes in oestrogen-degrading actinobacteria remain unidentified. In this study, we identified a gene cluster encoding several putative oestrogen-degrading genes (aed; actinobacterial oestrogen degradation) in actinobacterium Rhodococcus sp. strain B50. Among them, the aedA and aedB genes involved in oestrogenic A-ring cleavage were identified through gene-disruption experiments. We demonstrated that actinobacterial oestrone 4-hydroxylase (AedA) is a cytochrome P450-type monooxygenase. We also detected the accumulation of two extracellular oestrogenic metabolites, including pyridinestrone acid (PEA) and 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), in the oestrone-fed strain B50 cultures. Since actinobacterial aedB and proteobacterial edcB shared < 40% sequence identity, 4-hydroxyestrone 4,5-dioxygenase genes (namely aedB and edcB) could serve as a specific biomarker to differentiate the contribution of actinobacteria and proteobacteria in environmental oestrogen degradation. Therefore, 4-hydroxyestrone 4,5-dioxygenase genes and the extracellular metabolites PEA and HIP were used as biomarkers to investigate oestrogen biodegradation in an urban estuarine sediment. Interestingly, our data suggested that actinobacteria are active oestrogen degraders in the urban estuarine sediment.
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Affiliation(s)
| | - Yi‐Lung Chen
- Department of MicrobiologySoochow UniversityTaipei111Taiwan
| | - Menghsiao Meng
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | | | - Masae Horinouchi
- Condensed Molecular Materials LaboratoryRIKENSaitama351‐0198Japan
| | - Toshiaki Hayashi
- Environmental Molecular Biology LaboratoryRIKENSaitama351‐0198Japan
| | - Po‐Hsiang Wang
- Gradaute Institute of Environmental EngineeringNational Central UniversityTaoyuan320Taiwan
- Earth‐Life Science Institute (ELSI)Tokyo Institute of TechnologyTokyo145‐0061Japan
| | - Yin‐Ru Chiang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
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24
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Wei Z, Wang JJ, Fultz LM, White P, Jeong C. Application of biochar in estrogen hormone-contaminated and manure-affected soils: Impact on soil respiration, microbial community and enzyme activity. CHEMOSPHERE 2021; 270:128625. [PMID: 33077185 DOI: 10.1016/j.chemosphere.2020.128625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Biochar as a soil amendment has been proposed for enhancing carbon sequestration and manure-borne hormone contaminant remediation. However, little is known about the ecological risk of biochar application in the soil with hormone contamination. This study investigated the influence of biochar in three manure-impacted soils contaminated with estrogen hormones, natural estrogen 17β-estradiol and synthesized estrogen 17α-ethinylestradiol in a microcosm experiment. Specifically, microbial respiration was periodically determined during microcosm incubation while microbial community phospholipid fatty acids and activities of nutrient (C, N, P, S) cycling related enzymes (β-glucosidase, urease, phosphodiesterase, arylsulfatase) were characterized after the incubation. Results showed that the manure-impacted soils with high SOC generally had greater total microbial biomass, ratios of fungi/bacteria and Gram-positive bacteria/Gram-negative bacteria, and phosphodiesterase activity, but lower urease activity. Additionally, hormones stimulated microbial respiration and biomass, while had little impact on activity of the enzymes. On the other hand, biochar showed negative priming effect by significantly decreasing total microbial biomass by 8.7%-26.4%, CO2 production by 16.6%-33.5%, and glucosidase activity by 27.1%-41.0% in the three soils. Biochar significantly increased the activity of phosphodiesterase, showed no impact on arylsulfatase, while decreased the activity of urease. Overall, the study suggests that when used in hormone remediation in manure-impact soils, biochar could improve phosphodiesterase activity, but may decrease soil microbial activity and the activity of soil glucosidase and urease.
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Affiliation(s)
- Zhuo Wei
- School of Plant, Environment & Soil Sciences, Louisiana State University Agcenter, Baton Rouge, LA, 70803, United States
| | - Jim J Wang
- School of Plant, Environment & Soil Sciences, Louisiana State University Agcenter, Baton Rouge, LA, 70803, United States.
| | - Lisa M Fultz
- School of Plant, Environment & Soil Sciences, Louisiana State University Agcenter, Baton Rouge, LA, 70803, United States
| | - Paul White
- United States Department of Agriculture, Agriculture Research Service, Sugarcane Research Unit, Houma, LA, 70360, United States
| | - Changyoon Jeong
- Red River Research Station, Louisiana State University Agricultural Center, Bossier City, LA, 71112, United States
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25
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Feller FM, Marke G, Drees SL, Wöhlbrand L, Rabus R, Philipp B. Substrate Inhibition of 5β-Δ 4-3-Ketosteroid Dehydrogenase in Sphingobium sp. Strain Chol11 Acts as Circuit Breaker During Growth With Toxic Bile Salts. Front Microbiol 2021; 12:655312. [PMID: 33868213 PMCID: PMC8044976 DOI: 10.3389/fmicb.2021.655312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
In contrast to many steroid hormones and cholesterol, mammalian bile salts are 5β-steroids, which leads to a bent structure of the steroid core. Bile salts are surface-active steroids excreted into the environment in large amounts, where they are subject to bacterial degradation. Bacterial steroid degradation is initiated by the oxidation of the A-ring leading to canonical Δ4-3-keto steroids with a double bond in the A-ring. For 5β-bile salts, this Δ4-double bond is introduced into 3-keto-bile salts by a 5β-Δ4-ketosteroid dehydrogenase (5β-Δ4-KSTD). With the Nov2c019 protein from bile-salt degrading Sphingobium sp. strain Chol11, a novel 5β-Δ4-KSTD for bile-salt degradation belonging to the Old Yellow Enzyme family was identified and named 5β-Δ4-KSTD1. By heterologous production in Escherichia coli, 5β-Δ4-KSTD function could be shown for 5β-Δ4-KSTD1 as well as the homolog CasH from bile-salt degrading Rhodococcus jostii RHA1. The deletion mutant of 5β-Δ4-kstd1 had a prolonged lag-phase with cholate as sole carbon source and, in accordance with the function of 5β-Δ4-KSTD1, showed delayed 3-ketocholate transformation. Purified 5β-Δ4-KSTD1 was specific for 5β-steroids in contrast to 5α-steroids and converted steroids with a variety of hydroxy groups regardless of the presence of a side chain. 5β-Δ4-KSTD1 showed a relatively low K m for 3-ketocholate, a very high specific activity and pronounced substrate inhibition. With respect to the toxicity of bile salts, these kinetic properties indicate that 5β-Δ4-KSTD1 can achieve fast detoxification of the detergent character as well as prevention of an overflow of the catabolic pathway in presence of increased bile-salt concentrations.
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Affiliation(s)
- Franziska M Feller
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Gina Marke
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Steffen L Drees
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Bodo Philipp
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany.,Fraunhofer-Institut für Molekularbiologie und Angewandte Oekologie IME, Schmallenberg, Germany
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26
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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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27
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Hussain T, Murtaza G, Kalhoro DH, Kalhoro MS, Metwally E, Chughtai MI, Mazhar MU, Khan SA. Relationship between gut microbiota and host-metabolism: Emphasis on hormones related to reproductive function. ACTA ACUST UNITED AC 2021; 7:1-10. [PMID: 33997325 PMCID: PMC8110851 DOI: 10.1016/j.aninu.2020.11.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022]
Abstract
It has been well recognized that interactions between the gut microbiota and host-metabolism have a proven effect on health. The gut lumen is known for harboring different bacterial communities. Microbial by-products and structural components, which are derived through the gut microbiota, generate a signaling response to maintain homeostasis. Gut microbiota is not only involved in metabolic disorders, but also participates in the regulation of reproductive hormonal function. Bacterial phyla, which are localized in the gut, allow for the metabolization of steroid hormones through the stimulation of different enzymes. Reproductive hormones such as progesterone, estrogen and testosterone play a pivotal role in the successful completion of reproductive events. Disruption in this mechanism may lead to reproductive disorders. Environmental bacteria can affect the metabolism, and degrade steroid hormones and their relevant compounds. This behavior of the bacteria can safely be implemented to eliminate steroidal compounds from a polluted environment. In this review, we summarize the metabolism of steroid hormones on the regulation of gut microbiota and vice-versa, and also examined the significant influence this process has on various events of reproductive function. Altogether, the evidence suggests that steroid hormones and gut microbiota exert a central role in the modification of host bacterial action and impact the reproductive efficiency of animals and humans.
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Affiliation(s)
- Tarique Hussain
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, 38000, Pakistan
| | - Ghulam Murtaza
- Department of Animal Reproduction, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, Sindh, 70050, Pakistan
| | - Dildar H Kalhoro
- Department of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, Sindh, 70050, Pakistan
| | - Muhammad S Kalhoro
- Department of Animal Products Technology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, Sindh, 70050, Pakistan
| | - Elsayed Metwally
- Department of Cytology & Histology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Muhammad I Chughtai
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, 38000, Pakistan
| | - Muhammad U Mazhar
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, 38000, Pakistan
| | - Shahzad A Khan
- Faculty of Animal Husbandry and Veterinary Sciences, University of Poonch, Rawalakot, 12350, Pakistan
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Santalova EA, Denisenko VA, Dmitrenok PS. Structural Analysis of Oxidized Cerebrosides from the Extract of Deep-Sea Sponge Aulosaccus sp.: Occurrence of Amide-Linked Allylically Oxygenated Fatty Acids. Molecules 2020; 25:E6047. [PMID: 33371471 PMCID: PMC7767537 DOI: 10.3390/molecules25246047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 11/17/2022] Open
Abstract
The structural elucidation of primary and secondary peroxidation products, formed from complex lipids, is a challenge in lipid analysis. In the present study, rare minor oxidized cerebrosides, isolated from the extract of a far eastern deep-sea glass sponge, Aulosaccus sp., were analyzed as constituents of a multi-component RP-HPLC (high-performance liquid chromatography on reversed-phase column) fraction using NMR (nuclear magnetic resonance) spectroscopy, mass spectrometry, GC (gas chromatography), and chemical transformations (including hydrogenation or derivatization with dimethyl disulfide before hydrolysis). Eighteen previously unknown β-D-glucopyranosyl-(1→1)-ceramides (1a-a//, 1b-b//, 2a-a//, 2b-b//, 3c-c//, 3d-d//) were shown to contain phytosphingosine-type backbones (2S,3S,4R,11Z)-2-aminoeicos-11-ene-1,3,4-triol (in 1), (2S,3S,4R,13Z)-2-aminoeicos-13-ene-1,3,4-triol (in 2), and (13S*,14R*)-2-amino-13,14-methylene-eicosane-1,3,4-triol (in 3). These backbones were N-acylated with straight-chain monoenoic (2R)-2-hydroxy acids that had allylic hydroperoxy/hydroxy/keto groups on C-17/ in the 15/E-23:1 chain (a-a//), C-16/ in the 17/E-23:1 (b-b//) and 14/E-22:1 (c-c//) chains, and C-15/ in the 16/E-22:1 chain (d-d//). Utilizing complementary instrumental and chemical methods allowed for the first detailed structural analysis of a complex mixture of glycosphingolipids, containing allylically oxygenated monoenoic acyl chains.
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Affiliation(s)
- Elena A. Santalova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100 let Vladivostoku 159, 690022 Vladivostok, Russia; (V.A.D.); (P.S.D.)
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29
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Tsuji JM, Tran N, Schiff SL, Venkiteswaran JJ, Molot LA, Tank M, Hanada S, Neufeld JD. Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. THE ISME JOURNAL 2020; 14:2732-2747. [PMID: 32747714 PMCID: PMC7784702 DOI: 10.1038/s41396-020-0725-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/02/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022]
Abstract
Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - N Tran
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - S L Schiff
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - J J Venkiteswaran
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, N2L 3C5, Canada
| | - L A Molot
- York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - M Tank
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
- Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - S Hanada
- Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - J D Neufeld
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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Genome-Wide Transcriptome Profiling Provides Insight on Cholesterol and Lithocholate Degradation Mechanisms in Nocardioides simplex VKM Ac-2033D. Genes (Basel) 2020; 11:genes11101229. [PMID: 33092158 PMCID: PMC7593942 DOI: 10.3390/genes11101229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, Nocardioides simplex VKM Ac-2033D, were studied. Biochemical, transcriptomic, and bioinformatic approaches were used. Among the intermediates of sterol sidechain oxidation cholest-5-en-26-oic acid and 3-oxo-cholesta-1,4-dien-26-oic acid were identified as those that have not been earlier reported for N. simplex and related species. The transcriptomic approach revealed candidate genes of cholesterol and lithocholic acid (LCA) catabolism by the strain. A separate set of genes combined in cluster and additional 3-ketosteroid Δ1-dehydrogenase and 3-ketosteroid 9α-hydroxylases that might be involved in LCA catabolism were predicted. Bioinformatic calculations based on transcriptomic data showed the existence of a previously unknown transcription factor, which regulates cholate catabolism gene orthologs. The results contribute to the knowledge on diversity of steroid catabolism regulation in actinobacteria and might be used at the engineering of microbial catalysts for ecological and industrial biotechnology.
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31
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Wang H, Song S, Peng F, Yang F, Chen T, Li X, Cheng X, He Y, Huang Y, Su Z. Whole-genome and enzymatic analyses of an androstenedione-producing Mycobacterium strain with residual phytosterol-degrading pathways. Microb Cell Fact 2020; 19:187. [PMID: 33008397 PMCID: PMC7532642 DOI: 10.1186/s12934-020-01442-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 09/25/2020] [Indexed: 01/29/2023] Open
Abstract
Mycobacterium neoaurum strains can transform phytosterols to 4-androstene-3,17-dione (4-AD), a key intermediate for the synthesis of advanced steroidal medicines. In this work, we presented the complete genome sequence of the M. neoaurum strain HGMS2, which transforms β-sitosterol to 4-AD. Through genome annotation, a phytosterol-degrading pathway in HGMS2 was predicted and further shown to form a 9,10-secosteroid intermediate by five groups of enzymes. These five groups of enzymes included three cholesterol oxidases (ChoM; group 1: ChoM1, ChoM2 and Hsd), two monooxygenases (Mon; group 2: Mon164 and Mon197), a set of enzymes for side-chain degradation (group 3), one 3-ketosteroid-1,2-dehydrogenase (KstD; group 4: KstD211) and three 3-ketosteroid-9a-hydroxylases (Ksh; group 5: KshA226, KshA395 and KshB122). A gene cluster encoding Mon164, KstD211, KshA226, KshB122 and fatty acid β-oxidoreductases constituted one integrated metabolic pathway, while genes encoding other key enzymes were sporadically distributed. All key enzymes except those from group 3 were prepared as recombinant proteins and their activities were evaluated, and the proteins exhibited distinct activities compared with enzymes identified from other bacterial species. Importantly, we found that the KstD211 and KshA395 enzymes in the HGMS2 strain retained weak activities and caused the occurrence of two major impurities, i.e., 1,4-androstene-3,17-dione (ADD) and 9-hydroxyl-4-androstene-3,17-dione (9OH-AD) during β-sitosterol fermentation. The concurrence of these two 4-AD analogs not only lowered 4-AD production yield but also hampered 4-AD purification. HGMS2 has the least number of genes encoding KstD and Ksh enzymes compared with current industrial strains. Therefore, HGMS2 could be a potent strain by which the 4-AD production yield could be enhanced by disabling the KstD211 and KshA395 enzymes. Our work also provides new insight into the engineering of the HGMS2 strain to produce ADD and 9OH-AD for industrial application.
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Affiliation(s)
- Hongwei Wang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Shikui Song
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Fei Peng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Fei Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Tian Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Xin Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China.,Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan, 430075, Hubei, China
| | - Yijun He
- Hubei Goto Biotech Inc., No. 1 Baiguoshu Road, Shuidu Industrial Park, Danjiangkou, 442700, Hubei, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China. .,Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan, 430075, Hubei, China.
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32
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Spasov E, Tsuji JM, Hug LA, Doxey AC, Sauder LA, Parker WJ, Neufeld JD. High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. THE ISME JOURNAL 2020; 14:1857-1872. [PMID: 32332864 PMCID: PMC7305129 DOI: 10.1038/s41396-020-0650-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/03/2020] [Accepted: 03/30/2020] [Indexed: 01/31/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.
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Affiliation(s)
- Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Laura A Sauder
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Wayne J Parker
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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Chiang Y, Wei ST, Wang P, Wu P, Yu C. Microbial degradation of steroid sex hormones: implications for environmental and ecological studies. Microb Biotechnol 2020; 13:926-949. [PMID: 31668018 PMCID: PMC7264893 DOI: 10.1111/1751-7915.13504] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022] Open
Abstract
Steroid hormones modulate development, reproduction and communication in eukaryotes. The widespread occurrence and persistence of steroid hormones have attracted public attention due to their endocrine-disrupting effects on both wildlife and human beings. Bacteria are responsible for mineralizing steroids from the biosphere. Aerobic degradation of steroid hormones relies on O2 as a co-substrate of oxygenases to activate and to cleave the recalcitrant steroidal core ring. To date, two oxygen-dependent degradation pathways - the 9,10-seco pathway for androgens and the 4,5-seco pathways for oestrogens - have been characterized. Under anaerobic conditions, denitrifying bacteria adopt the 2,3-seco pathway to degrade different steroid structures. Recent meta-omics revealed that microorganisms able to degrade steroids are highly diverse and ubiquitous in different ecosystems. This review also summarizes culture-independent approaches using the characteristic metabolites and catabolic genes to monitor steroid biodegradation in various ecosystems.
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Affiliation(s)
- Yin‐Ru Chiang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
| | | | - Po‐Hsiang Wang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
- Present address:
Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - Pei‐Hsun Wu
- Graduate Institute of Environmental EngineeringNational Taiwan UniversityTaipei106Taiwan
| | - Chang‐Ping Yu
- Graduate Institute of Environmental EngineeringNational Taiwan UniversityTaipei106Taiwan
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34
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Liu N, Shi YE, Li J, Zhu M, Zhang T. Isolation and characterization of a new highly effective 17β-estradiol-degrading Gordonia sp. strain R9. 3 Biotech 2020; 10:174. [PMID: 32206508 DOI: 10.1007/s13205-020-2156-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/27/2020] [Indexed: 01/27/2023] Open
Abstract
In this report, Gordonia sp. strain R9 isolated from an enrichment culture of chicken leachate was confirmed to degrade 17β-estradiol (E2), which can also use other estrogens (estrone, estriol, and 17α-ethynylestradiol) and testosterone as sole carbon and energy sources. Optimization of growth conditions showed that Gordonia sp. strain R9 can tolerate a very wide range of temperature (4-40 °C) and pH (1.0-11.0), and is sensitive to antibiotics including kanamycin, ampicillin, chloramphenicol, and carbenicillin. Optimal culture conditions for E2 degradation were 30 °C and pH 7.0 with almost 100% degradation of E2 concentrations ranging from 50 µg/L to 5 mg/L within 24 h. The E2 intermediates so generated included estrone (E1), estratriol (E3), (3Z)-3-(3-hydroxy-3a-methyl-7-oxododecahydro-6H-cyclopenta[a]naphthalen-6-ylidene) propanoic acid and 3-hydroxy-3a-methyl-7-oxododecahydro-1H-cyclopenta[a]naphthalene-6-carboxylic acid. These results indicate that the highly effective E2-degradative ability of Gordonia sp. strain R9 merits further investigation as a candidate for large-scale estrogen biodegradation.
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Affiliation(s)
- Na Liu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130021 China
| | - Yue-E Shi
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130021 China
| | - Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130021 China
| | - Meiling Zhu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130021 China
| | - Tingdi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130021 China
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35
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Grazon C, Baer RC, Kuzmanović U, Nguyen T, Chen M, Zamani M, Chern M, Aquino P, Zhang X, Lecommandoux S, Fan A, Cabodi M, Klapperich C, Grinstaff MW, Dennis AM, Galagan JE. A progesterone biosensor derived from microbial screening. Nat Commun 2020; 11:1276. [PMID: 32152281 PMCID: PMC7062782 DOI: 10.1038/s41467-020-14942-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/03/2020] [Indexed: 01/08/2023] Open
Abstract
Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Uroš Kuzmanović
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Thuy Nguyen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Marjon Zamani
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Xiaoman Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | | | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Mark W Grinstaff
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - James E Galagan
- Department of Microbiology, Boston University, Boston, MA, 02118, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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36
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Pratush A, Ye X, Yang Q, Kan J, Peng T, Wang H, Huang T, Xiong G, Hu Z. Biotransformation strategies for steroid estrogen and androgen pollution. Appl Microbiol Biotechnol 2020; 104:2385-2409. [PMID: 31993703 DOI: 10.1007/s00253-020-10374-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 12/21/2022]
Abstract
The common steroid hormones are estrone (E1), 17β-estradiol (E2), estriol (E3), 17α-ethinylestradiol (EE2), and testosterone (T). These steroids are reported to contaminate the environment through wastewater treatment plants. Steroid estrogens are widespread in the aquatic environment and therefore pose a potential risk, as exposure to these compounds has adverse impacts on vertebrates. Excessive exposure to steroid estrogens causes endocrine disruption in aquatic vertebrates, which affects the normal sexual life of these animals. Steroid pollutants also cause several health problems in humans and other animals. Microbial degradation is an efficient method for removing hormone pollutants from the environment by remediation. Over the last two decades, microbial metabolism of steroids has gained considerable attention due to its higher efficiency to reduce pollutants from the environment. The present review is focused on the major causes of steroid pollution, concentrations of these pollutants in surface water, groundwater, drinking water, and wastewater, their effect on humans and aquatic animals, as well as recent efforts by various research groups that seek better ways to degrade steroids by aerobic and anaerobic microbial systems. Detailed overview of aerobic and anaerobic microbial biotransformation of steroid estrogens and testosterone present in the environment along with the active enzyme systems involved in these biotransformation reactions is described in the review article, which helps readers to understand the biotransformation mechanism of steroids in depth. Other measures such as co-metabolic degradation, consortia degradation, algal, and fungal steroid biotransformation are also discussed in detail.
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Affiliation(s)
- Amit Pratush
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Xueying Ye
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Qi Yang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jie Kan
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Tao Peng
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Tongwang Huang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Guangming Xiong
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School, Schleswig-Holstein, Campus Kiel, Brunswiker Str. 10, 24105, Kiel, Germany
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China.
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37
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Steryl Ester Formation and Accumulation in Steroid-Degrading Bacteria. Appl Environ Microbiol 2020; 86:AEM.02353-19. [PMID: 31704679 DOI: 10.1128/aem.02353-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022] Open
Abstract
Steryl esters (SEs) are important storage compounds in many eukaryotes and are often prominent components of intracellular lipid droplets. Here, we demonstrate that selected Actino- and Proteobacteria growing on sterols are also able to synthesize SEs and to sequester them in cytoplasmic lipid droplets. We found cholesteryl ester (CE) formation in members of the actinobacterial genera Rhodococcus, Mycobacterium, and Amycolatopsis, as well as several members of the proteobacterial Cellvibrionales order. CEs maximally accumulated under nitrogen-limiting conditions, suggesting that steryl ester formation plays a crucial role for storing excess energy and carbon under adverse conditions. Rhodococcus jostii RHA1 was able to synthesize phytosteryl and cholesteryl esters, the latter reaching up to 7% of its cellular dry weight and 69% of its lipid droplets. Purified lipid droplets from RHA1 contained CEs, free cholesterol, and triacylglycerols. In addition, we found formation of CEs in Mycobacterium tuberculosis when it was grown with cholesterol plus an additional fatty acid substrate. This study provides a basis for the application of bacterial whole-cell systems in the biotechnological production of SEs for use in functional foods and cosmetics.IMPORTANCE Oleaginous bacteria exhibit great potential for the production of high-value neutral lipids, such as triacylglycerols and wax esters. This study describes the formation of steryl esters (SEs) as neutral lipid storage compounds in sterol-degrading oleaginous bacteria, providing a basis for biotechnological production of SEs using bacterial systems with potential applications in the functional food, nutraceutical, and cosmetic industries. We found cholesteryl ester (CE) formation in several sterol-degrading Actino- and Proteobacteria under nitrogen-limiting conditions, suggesting an important role of this process in storing energy and carbon under adverse conditions. In addition, Mycobacterium tuberculosis grown on cholesterol accumulated CEs in the presence of an additional fatty acid substrate.
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38
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Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation. Proc Natl Acad Sci U S A 2019; 117:1395-1403. [PMID: 31848239 DOI: 10.1073/pnas.1914380117] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroid estrogens modulate physiology and development of vertebrates. Conversion of C19 androgens into C18 estrogens is thought to be an irreversible reaction. Here, we report a denitrifying Denitratisoma sp. strain DHT3 capable of catabolizing estrogens or androgens anaerobically. Strain DHT3 genome contains a polycistronic gene cluster, emtABCD, differentially transcribed under estrogen-fed conditions and predicted to encode a cobalamin-dependent methyltransferase system conserved among estrogen-utilizing anaerobes; an emtA-disrupted DHT3 derivative could catabolize androgens but not estrogens. These data, along with the observed androgen production in estrogen-fed strain DHT3 cultures, suggested the occurrence of a cobalamin-dependent estrogen methylation to form androgens. Consistently, the estrogen conversion into androgens in strain DHT3 cell extracts requires methylcobalamin and is inhibited by propyl iodide, a specific inhibitor of cobalamin-dependent enzymes. The identification of the cobalamin-dependent estrogen methylation thus represents an unprecedented metabolic link between cobalamin and steroid metabolism and suggests that retroconversion of estrogens into androgens occurs in the biosphere.
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39
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Joyce SA, Kamil A, Fleige L, Gahan CGM. The Cholesterol-Lowering Effect of Oats and Oat Beta Glucan: Modes of Action and Potential Role of Bile Acids and the Microbiome. Front Nutr 2019; 6:171. [PMID: 31828074 PMCID: PMC6892284 DOI: 10.3389/fnut.2019.00171] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Consumption of sufficient quantities of oat products has been shown to reduce host cholesterol and thereby modulate cardiovascular disease risk. The effects are proposed to be mediated by the gel-forming properties of oat β-glucan which modulates host bile acid and cholesterol metabolism and potentially removes intestinal cholesterol for excretion. However, the gut microbiota has emerged as a major factor regulating cholesterol metabolism in the host. Oat β-glucan has been shown to modulate the gut microbiota, particularly those bacterial species that influence host bile acid metabolism and production of short chain fatty acids, factors which are regulators of host cholesterol homeostasis. Given a significant role for the gut microbiota in cholesterol metabolism it is likely that the effects of oat β-glucan on the host are multifaceted and involve regulation of microbe-host interactions at the gut interface. Here we consider the potential for oat β-glucan to influence microbial populations in the gut with potential consequences for bile acid metabolism, reverse cholesterol transport (RCT), short-chain fatty acid (SCFA) production, bacterial metabolism of cholesterol and microbe-host signaling.
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Affiliation(s)
- Susan A Joyce
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Alison Kamil
- Quaker Oats Center of Excellence, PepsiCo R&D Nutrition, Barrington, IL, United States
| | - Lisa Fleige
- Quaker Oats Center of Excellence, PepsiCo R&D Nutrition, Barrington, IL, United States
| | - Cormac G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,School of Pharmacy, University College Cork, Cork, Ireland
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40
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Testosterone Degradative Pathway of Novosphingobium tardaugens. Genes (Basel) 2019; 10:genes10110871. [PMID: 31683600 PMCID: PMC6895838 DOI: 10.3390/genes10110871] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/16/2019] [Accepted: 10/28/2019] [Indexed: 01/25/2023] Open
Abstract
In this work, we have shown that Novosphingobium tardaugens NBRC 16725 (strain ARI-1), a bacterial strain that was isolated due to its capacity to mineralize the estrogenic endocrine compound 17β-estradiol, is also able to mineralize testosterone, the androgenic endocrine compound. Using in silico analysis, we predicted a new putative steroid degradation (SD) gene cluster in strain ARI-1, which resembles genes involved in testosterone degradation in Comamonas testosteroni and other testosterone degrading bacteria like Actinobacteria (like Rhodococcus and Mycobacteria genera) although with significant differences in gene organization. A whole transcriptomic analysis of N. tardaugens revealed that testosterone produces a limited induction of the genes of the SD cluster that show a high basal expression in its absence. The 3β/17β-hydroxysteroid dehydrogenase involved in the first metabolic step of testosterone degradation was identified by using genetic and biochemical approaches. The construction of knockout mutant strains in the genes of the SD cluster together with in silico analyses suggests the existence of gene redundancy in the genome of N. tardaugens. This work will expand the knowledge about the metabolic pathways and biotransformation capabilities of a Gram-negative bacterium that could become a new model system in the bacterial steroid degradation field.
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41
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Birolli WG, Lima RN, Porto ALM. Applications of Marine-Derived Microorganisms and Their Enzymes in Biocatalysis and Biotransformation, the Underexplored Potentials. Front Microbiol 2019; 10:1453. [PMID: 31481935 PMCID: PMC6710449 DOI: 10.3389/fmicb.2019.01453] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Biodiversity has been explored in the search for novel enzymes, including forests, savannas, tundras, deserts, and finally the sea. Marine microorganisms and their enzymes are capable of being active in high-salt concentration, large range of temperature, and high incidence of light and pressure, constituting an important source of unique biocatalysts. This review presents studies employing whole-cell processes of marine bacteria and fungi, aiming for new catalysts for different reactions in organic synthesis, such as reduction, oxidation, hydroxylation, hydrolysis, elimination, and conjugation. Genomics and protein engineering studies were also approached, and reactions employing isolated enzymes from different classes (oxidoreductases, hydrolases, lyases, and ligases) were described and summarized. Future biotechnological studies and process development should focus on molecular biology for the obtention of enzymes with interesting, fascinating and enhanced properties, starting from the exploration of microorganisms from the marine environment. This review approaches the literature about the use of marine-derived bacteria, fungi, and their enzymes for biocatalytic reactions of organic compounds, promoting a discussion about the possibilities of these microorganisms in the synthesis of different substances.
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Affiliation(s)
- Willian G Birolli
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil.,Center of Exact Sciences and Technology, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - Rafaely N Lima
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil.,Center of Exact Sciences and Technology, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - André L M Porto
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil
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42
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Microbial transformation of cholesterol: reactions and practical aspects-an update. World J Microbiol Biotechnol 2019; 35:131. [PMID: 31432251 DOI: 10.1007/s11274-019-2708-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/03/2019] [Indexed: 12/11/2022]
Abstract
Cholesterol is a C27-sterol employed as starting material for the synthesis of valuable pharmaceutical steroids and precursors. The microbial transformations of cholesterol have been widely studied, since they are performed with high regio- and stereoselectivity and allow the production of steroidal compounds which are difficult to synthesize by classical chemical methods. In recent years, ongoing research is being conducted to discover novel biocatalysts and to develop biotechnological processes to improve existing biocatalysts and biotransformation reactions. The main objective of this review is to present the most remarkable advances in fungal and bacterial transformation of cholesterol, focusing on the different types of microbial reactions and biocatalysts, biotransformation products, and practical aspects related to sterol dispersion improvement, covering literature since 2000. It reviews the conversion of cholesterol by whole-cell biocatalysts and by purified enzymes that lead to various structural modifications, including side chain cleavage, hydroxylation, dehydrogenation/reduction, isomerization and esterification. Finally, approaches used to improve the poor solubility of cholesterol in aqueous media, such as the use of different sterol-solubilizing agents or two-phase conversion system, are also discussed.
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43
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Mendelski MN, Dölling R, Feller FM, Hoffmann D, Ramos Fangmeier L, Ludwig KC, Yücel O, Mährlein A, Paul RJ, Philipp B. Steroids originating from bacterial bile acid degradation affect Caenorhabditis elegans and indicate potential risks for the fauna of manured soils. Sci Rep 2019; 9:11120. [PMID: 31366938 PMCID: PMC6668416 DOI: 10.1038/s41598-019-47476-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/15/2019] [Indexed: 02/08/2023] Open
Abstract
Bile acids are steroid compounds from the digestive tracts of vertebrates that enter agricultural environments in unusual high amounts with manure. Bacteria degrading bile acids can readily be isolated from soils and waters including agricultural areas. Under laboratory conditions, these bacteria transiently release steroid compounds as degradation intermediates into the environment. These compounds include androstadienediones (ADDs), which are C19-steroids with potential hormonal effects. Experiments with Caenorhabditis elegans showed that ADDs derived from bacterial bile acid degradation had effects on its tactile response, reproduction rate, and developmental speed. Additional experiments with a deletion mutant as well as transcriptomic analyses indicated that these effects might be conveyed by the putative testosterone receptor NHR-69. Soil microcosms showed that the natural microflora of agricultural soil is readily induced for bile acid degradation accompanied by the transient release of steroid intermediates. Establishment of a model system with a Pseudomonas strain and C. elegans in sand microcosms indicated transient release of ADDs during the course of bile acid degradation and negative effects on the reproduction rate of the nematode. This proof-of-principle study points at bacterial degradation of manure-derived bile acids as a potential and so-far overlooked risk for invertebrates in agricultural soils.
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Affiliation(s)
- M N Mendelski
- Institute of Zoophysiology, University of Münster (WWU), Münster, Germany
| | - R Dölling
- Institute of Zoophysiology, University of Münster (WWU), Münster, Germany
| | - F M Feller
- Institute of Molecular Microbiology and Biotechnology, University of Münster (WWU), Münster, Germany
| | - D Hoffmann
- Institute of Zoophysiology, University of Münster (WWU), Münster, Germany
| | - L Ramos Fangmeier
- Institute of Zoophysiology, University of Münster (WWU), Münster, Germany
| | - K C Ludwig
- Institute of Molecular Microbiology and Biotechnology, University of Münster (WWU), Münster, Germany.,Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - O Yücel
- Institute of Molecular Microbiology and Biotechnology, University of Münster (WWU), Münster, Germany
| | - A Mährlein
- Institute of Molecular Microbiology and Biotechnology, University of Münster (WWU), Münster, Germany
| | - R J Paul
- Institute of Zoophysiology, University of Münster (WWU), Münster, Germany
| | - B Philipp
- Institute of Molecular Microbiology and Biotechnology, University of Münster (WWU), Münster, Germany.
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44
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Guevara G, Olortegui Flores Y, Fernández de las Heras L, Perera J, Navarro Llorens JM. Metabolic engineering of Rhodococcus ruber Chol-4: A cell factory for testosterone production. PLoS One 2019; 14:e0220492. [PMID: 31348804 PMCID: PMC6660089 DOI: 10.1371/journal.pone.0220492] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 11/30/2022] Open
Abstract
Rhodococcus ruber Chol-4 is a potent steroid degrader that has a great potential as a biotechnological tool. As proof of concept, this work presents testosterone production from 4-androstene-3,17-dione by tailoring innate catabolic enzymes of the steroid catabolism inside the strain. A R. ruber quadruple mutant was constructed in order to avoid the breakage of the steroid nucleus. At the same time, an inducible expression vector for this strain was developed. The 17-ketoreductase gene from the fungus Cochliobolus lunatus was cloned and overexpressed in this vector. The engineered strain was able to produce testosterone from 4-androstene-3,17-dione using glucose for cofactor regeneration with a molar conversion of 61%. It is important to note that 91% of the testosterone was secreted outside the cell after 3 days of cell biotransformation. The results support the idea that Rhodococcus ruber Chol-4 can be metabolically engineered and can be used for the production of steroid intermediates.
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Affiliation(s)
- Govinda Guevara
- Department of Biochemistry and Molecular Biology, Facultad de CC, Biológicas, C/Jose Antonio Novais, Universidad Complutense de Madrid, Madrid, Spain
| | - Yamileth Olortegui Flores
- Department of Biochemistry and Molecular Biology, Facultad de CC, Biológicas, C/Jose Antonio Novais, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Fernández de las Heras
- Department of Biochemistry and Molecular Biology, Facultad de CC, Biológicas, C/Jose Antonio Novais, Universidad Complutense de Madrid, Madrid, Spain
| | - Julián Perera
- Department of Biochemistry and Molecular Biology, Facultad de CC, Biológicas, C/Jose Antonio Novais, Universidad Complutense de Madrid, Madrid, Spain
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de CC, Biológicas, C/Jose Antonio Novais, Universidad Complutense de Madrid, Madrid, Spain
- * E-mail:
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45
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Olivera ER, Luengo JM. Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways. Genes (Basel) 2019; 10:genes10070512. [PMID: 31284586 PMCID: PMC6678751 DOI: 10.3390/genes10070512] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Steroids are perhydro-1,2-cyclopentanophenanthrene derivatives that are almost exclusively synthesised by eukaryotic organisms. Since the start of the Anthropocene, the presence of these molecules, as well as related synthetic compounds (ethinylestradiol, dexamethasone, and others), has increased in different habitats due to farm and municipal effluents and discharge from the pharmaceutical industry. In addition, the highly hydrophobic nature of these molecules, as well as the absence of functional groups, makes them highly resistant to biodegradation. However, some environmental bacteria are able to modify or mineralise these compounds. Although steroid-metabolising bacteria have been isolated since the beginning of the 20th century, the genetics and catabolic pathways used have only been characterised in model organisms in the last few decades. Here, the metabolic alternatives used by different bacteria to metabolise steroids (e.g., cholesterol, bile acids, testosterone, and other steroid hormones), as well as the organisation and conservation of the genes involved, are reviewed.
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Affiliation(s)
- Elías R Olivera
- Departamento Biología Molecular (Área Bioquímica y Biología Molecular), Universidad de León, 24007 León, Spain.
| | - José M Luengo
- Departamento Biología Molecular (Área Bioquímica y Biología Molecular), Universidad de León, 24007 León, Spain
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46
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Bragin EY, Shtratnikova VY, Schelkunov MI, Dovbnya DV, Donova MV. Genome-wide response on phytosterol in 9-hydroxyandrostenedione-producing strain of Mycobacterium sp. VKM Ac-1817D. BMC Biotechnol 2019; 19:39. [PMID: 31238923 PMCID: PMC6593523 DOI: 10.1186/s12896-019-0533-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
Background Aerobic side chain degradation of phytosterols by actinobacteria is the basis for the industrial production of androstane steroids which are the starting materials for the synthesis of steroid hormones. A native strain of Mycobacterium sp. VKM Ac-1817D effectively produces 9α-hydroxyandrost-4-ene-3,17-dione (9-OH-AD) from phytosterol, but also is capable of slow steroid core degradation. However, the set of the genes with products that are involved in phytosterol oxidation, their organisation and regulation remain poorly understood. Results High-throughput sequencing of the global transcriptomes of the Mycobacterium sp. VKM Ac-1817D cultures grown with or without phytosterol was carried out. In the presence of phytosterol, the expression of 260 genes including those related to steroid catabolism pathways significantly increased. Two of the five genes encoding the oxygenase unit of 3-ketosteroid-9α-hydroxylase (kshA) were highly up-regulated in response to phytosterol (55- and 25-fold, respectively) as well as one of the two genes encoding its reductase subunit (kshB) (40-fold). Only one of the five putative genes encoding 3-ketosteroid-∆1-dehydrogenase (KstD_1) was up-regulated in the presence of phytosterol (61-fold), but several substitutions in the conservative positions of its product were revealed. Among the genes over-expressed in the presence of phytosterol, several dozen genes did not possess binding sites for the known regulatory factors of steroid catabolism. In the promoter regions of these genes, a regularly occurring palindromic motif was revealed. The orthologue of TetR-family transcription regulator gene Rv0767c of M. tuberculosis was identified in Mycobacterium sp. VKM Ac-1817D as G155_05115. Conclusions High expression levels of the genes related to the sterol side chain degradation and steroid 9α-hydroxylation in combination with possible defects in KstD_1 may contribute to effective 9α-hydroxyandrost-4-ene-3,17-dione accumulation from phytosterol provided by this biotechnologically relevant strain. The TetR-family transcription regulator gene G155_05115 presumably associated with the regulation of steroid catabolism. The results are of significance for the improvement of biocatalytic features of the microbial strains for the steroid industry. Electronic supplementary material The online version of this article (10.1186/s12896-019-0533-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugeny Y Bragin
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences", Nauki, 5, Pushchino, Russian Federation, 142290. .,Pharmins Ltd., Institutskaya, 4, Pushchino, Russian Federation, 142290.
| | - Victoria Y Shtratnikova
- A.N. Belozersky Research Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, 1, building 40, Moscow, Russian Federation, 119992
| | - Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Nobelya, 3, Moscow, Russian Federation, 121205.,Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny, 19, build. 1, Moscow, Russian Federation, 127051
| | - Dmitry V Dovbnya
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences", Nauki, 5, Pushchino, Russian Federation, 142290.,Pharmins Ltd., Institutskaya, 4, Pushchino, Russian Federation, 142290
| | - Marina V Donova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences", Nauki, 5, Pushchino, Russian Federation, 142290.,Pharmins Ltd., Institutskaya, 4, Pushchino, Russian Federation, 142290
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47
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Fieweger RA, Wilburn KM, VanderVen BC. Comparing the Metabolic Capabilities of Bacteria in the Mycobacterium tuberculosis Complex. Microorganisms 2019; 7:E177. [PMID: 31216777 PMCID: PMC6617402 DOI: 10.3390/microorganisms7060177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 02/06/2023] Open
Abstract
Pathogenic mycobacteria are known for their ability to maintain persistent infections in various mammals. The canonical pathogen in this genus is Mycobacterium tuberculosis and this bacterium is particularly successful at surviving and replicating within macrophages. Here, we will highlight the metabolic processes that M. tuberculosis employs during infection in macrophages and compare these findings with what is understood for other pathogens in the M. tuberculosis complex.
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Affiliation(s)
- Rachael A Fieweger
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Kaley M Wilburn
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
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48
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Guevara G, Castillo Lopez M, Alonso S, Perera J, Navarro-Llorens JM. New insights into the genome of Rhodococcus ruber strain Chol-4. BMC Genomics 2019; 20:332. [PMID: 31046661 PMCID: PMC6498646 DOI: 10.1186/s12864-019-5677-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 04/08/2019] [Indexed: 11/22/2022] Open
Abstract
Background Rhodococcus ruber strain Chol-4, a strain isolated from a sewage sludge sample, is able to grow in minimal medium supplemented with several compounds, showing a broad catabolic capacity. We have previously determined its genome sequence but a more comprehensive study of their metabolic capacities was necessary to fully unravel its potential for biotechnological applications. Results In this work, the genome of R. ruber strain Chol-4 has been re-sequenced, revised, annotated and compared to other bacterial genomes in order to investigate the metabolic capabilities of this microorganism. The analysis of the data suggests that R. ruber Chol-4 contains several putative metabolic clusters of biotechnological interest, particularly those involved on steroid and aromatic compounds catabolism. To demonstrate some of its putative metabolic abilities, R. ruber has been cultured in minimal media containing compounds belonging to several of the predicted metabolic pathways. Moreover, mutants were built to test the naphtalen and protocatechuate predicted catabolic gene clusters. Conclusions The genomic analysis and experimental data presented in this work confirm the metabolic potential of R. ruber strain Chol-4. This strain is an interesting model bacterium due to its biodegradation capabilities. The results obtained in this work will facilitate the application of this strain as a biotechnological tool. Electronic supplementary material The online version of this article (10.1186/s12864-019-5677-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Govinda Guevara
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
| | - Maria Castillo Lopez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Sergio Alonso
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Carretera de Can Ruti S/N 08916 Badalona, Barcelona, Spain
| | - Julián Perera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juana María Navarro-Llorens
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
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49
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Hollister EB, Oezguen N, Chumpitazi BP, Luna RA, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta TA, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagn 2019; 21:449-461. [PMID: 31005411 PMCID: PMC6504675 DOI: 10.1016/j.jmoldx.2019.01.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/30/2018] [Accepted: 01/06/2019] [Indexed: 02/06/2023] Open
Abstract
Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.
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Affiliation(s)
- Emily B Hollister
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Diversigen, Inc., Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Bruno P Chumpitazi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas
| | - Ruth Ann Luna
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Erica M Weidler
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas; Children's Nutrition Research Center, Houston, Texas
| | - Michelle Rubio-Gonzales
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Mahmoud Dahdouli
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Julia L Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Toni-Ann Mistretta
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Sabeen Raza
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Margaret Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, Washington
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas; Children's Nutrition Research Center, Houston, Texas
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas.
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Sowani H, Kulkarni M, Zinjarde S. Harnessing the catabolic versatility of Gordonia species for detoxifying pollutants. Biotechnol Adv 2019; 37:382-402. [DOI: 10.1016/j.biotechadv.2019.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/12/2019] [Accepted: 02/11/2019] [Indexed: 11/26/2022]
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