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McMillan AS, Foley MH, Perkins CE, Theriot CM. Loss of Bacteroides thetaiotaomicron bile acid-altering enzymes impacts bacterial fitness and the global metabolic transcriptome. Microbiol Spectr 2024; 12:e0357623. [PMID: 38018975 PMCID: PMC10783122 DOI: 10.1128/spectrum.03576-23] [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: 10/04/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Recent work on bile salt hydrolases (BSHs) in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it are not well understood. In this study, we set out to define if and how Bacteroides thetaiotaomicron (B. theta) uses its BSHs and hydroxysteroid dehydrogenase to modify bile acids to provide a fitness advantage for itself in vitro and in vivo. Genes encoding bile acid-altering enzymes were able to impact how B. theta responds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci. This suggests that B. theta may be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut.
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Affiliation(s)
- Arthur S. McMillan
- Department of Biological Sciences, Genetics Program, College of Science, North Carolina State University, Raleigh, North Carolina, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Matthew H. Foley
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Caroline E. Perkins
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Pan Y, Zhang H, Li M, He T, Guo S, Zhu L, Tan J, Wang B. Novel approaches in IBD therapy: targeting the gut microbiota-bile acid axis. Gut Microbes 2024; 16:2356284. [PMID: 38769683 PMCID: PMC11110704 DOI: 10.1080/19490976.2024.2356284] [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: 01/10/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and recurrent condition affecting the gastrointestinal tract. Disturbed gut microbiota and abnormal bile acid (BA) metabolism are notable in IBD, suggesting a bidirectional relationship. Specifically, the diversity of the gut microbiota influences BA composition, whereas altered BA profiles can disrupt the microbiota. IBD patients often exhibit increased primary bile acid and reduced secondary bile acid concentrations due to a diminished bacteria population essential for BA metabolism. This imbalance activates BA receptors, undermining intestinal integrity and immune function. Consequently, targeting the microbiota-BA axis may rectify these disturbances, offering symptomatic relief in IBD. Here, the interplay between gut microbiota and bile acids (BAs) is reviewed, with a particular focus on the role of gut microbiota in mediating bile acid biotransformation, and contributions of the gut microbiota-BA axis to IBD pathology to unveil potential novel therapeutic avenues for IBD.
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Affiliation(s)
- Yinping Pan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Haojie Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Tingjing He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Sihao Guo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological & Chemical engineering, Chongqing University of Education, Chongqing, PR China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
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Luu HN, Tran CTD, Wang R, Nguyen MVT, Tran MT, Tuong TTV, Tran QH, Le LC, Pham HTT, Vu HH, Bui NC, Ha HTT, Trinh DT, Thomas CE, Adams-Haduch J, Velikokhatnaya L, Schoen RE, Xie G, Jia W, Boffetta P, Clemente JC, Yuan JM. Associations between Ileal Juice Bile Acids and Colorectal Advanced Adenoma. Nutrients 2023; 15:2930. [PMID: 37447256 DOI: 10.3390/nu15132930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND There is an urgent need to identify biomarkers for advanced adenoma, an important precursor of colorectal cancer (CRC). We aimed to determine alterations in ileal juice bile acids associated with colorectal advanced adenoma. METHODS We quantified a comprehensive panel of primary and secondary bile acids and their conjugates using an ultraperformance liquid chromatography triple-quadrupole mass spectrometric assay in ileal juice collected at colonoscopy from 46 study subjects (i.e., 14 biopsy-confirmed advanced adenomas and 32 controls free of adenoma or cancer). Using analysis of covariance (ANCOVA), we examined the differences in bile acid concentrations by disease status, adjusting for age, sex, body mass index, smoking status and type 2 diabetes. RESULTS The concentrations of hyodeoxycholic acid (HCA) species in ileal juice of the advanced adenoma patients (geometric mean = 4501.9 nM) were significantly higher than those of controls (geometric mean = 1292.3 nM, p = 0.001). The relative abundance of ursodeoxycholic acid (UDCA) in total bile acids was significantly reduced in cases than controls (0.73% in cases vs. 1.33% in controls; p = 0.046). No significant difference between cases and controls was observed for concentrations of total or specific primary bile acids (i.e., cholic acid (CA), chenodeoxycholic acid (CDCA) and their glycine- and taurine-conjugates) and total and specific major secondary bile acids (i.e., deoxycholic acid and lithocholic acid). CONCLUSIONS Colorectal advanced adenoma was associated with altered bile acids in ileal juice. The HCA species may promote the development of colorectal advanced adenoma, whereas gut microbiota responsible for the conversion of CDCA to UDCA may protect against it. Our findings have important implications for the use of bile acids as biomarkers in early detection of colorectal cancer.
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Affiliation(s)
- Hung N Luu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chi Thi-Du Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
- College of Health Sciences, VinUniversity (VinUni), Hanoi 10000, Vietnam
- Center of Applied Sciences, Regenerative Medicine and Advanced Technologies, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Renwei Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Mai Vu-Tuyet Nguyen
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Mo Thi Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Thuy Thi-Van Tuong
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Quang Hong Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Linh Cu Le
- College of Health Sciences, VinUniversity (VinUni), Hanoi 10000, Vietnam
| | - Huong Thi-Thu Pham
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Hien Huy Vu
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Nam Chi Bui
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Hien Thi-Thu Ha
- Department of Cytopathology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Dung Tuan Trinh
- Department of Cytopathology, Vinmec Healthcare System, Hanoi 10000, Vietnam
- Department of Cytopathology, Tam Anh General Hospital, Hanoi 10000, Vietnam
| | - Claire E Thomas
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | | | | | - Robert E Schoen
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Guoxiang Xie
- University of Hawai'i Cancer Center, University of Hawaii, Honolulu, HI 96813, USA
| | - Wei Jia
- University of Hawai'i Cancer Center, University of Hawaii, Honolulu, HI 96813, USA
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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McMillan AS, Foley MH, Perkins CE, Theriot CM. Loss of Bacteroides thetaiotaomicron bile acid altering enzymes impact bacterial fitness and the global metabolic transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546749. [PMID: 37425690 PMCID: PMC10327073 DOI: 10.1101/2023.06.27.546749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Bacteroides thetaiotaomicron (B. theta) is a Gram-negative gut bacterium that encodes enzymes that alter the bile acid pool in the gut. Primary bile acids are synthesized by the host liver and are modified by gut bacteria. B. theta encodes two bile salt hydrolases (BSHs), as well as a hydroxysteroid dehydrogenase (HSDH). We hypothesize that B. theta modifies the bile acid pool in the gut to provide a fitness advantage for itself. To investigate each gene's role, different combinations of genes encoding bile acid altering enzymes (bshA, bshB, and hsdhA) were knocked out by allelic exchange, including a triple KO. Bacterial growth and membrane integrity assays were done in the presence and absence of bile acids. To explore if B. theta's response to nutrient limitation changes due to the presence of bile acid altering enzymes, RNASeq analysis of WT and triple KO strains in the presence and absence of bile acids was done. WT B. theta is more sensitive to deconjugated bile acids (CA, CDCA, and DCA) compared to the triple KO, which also decreased membrane integrity. The presence of bshB is detrimental to growth in conjugated forms of CDCA and DCA. RNA-Seq analysis also showed bile acid exposure impacts multiple metabolic pathways in B. theta, but DCA significantly increases expression of many genes in carbohydrate metabolism, specifically those in polysaccharide utilization loci or PULs, in nutrient limited conditions. This study suggests that bile acids B. theta encounters in the gut may signal the bacteria to increase or decrease its utilization of carbohydrates. Further study looking at the interactions between bacteria, bile acids, and the host may inform rationally designed probiotics and diets to ameliorate inflammation and disease. Importance Recent work on BSHs in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it is not well understood. In this study we set out to define if and how B. theta uses its BSHs and HSDH to modify bile acids to provide a fitness advantage for itself in vitro and in vivo. Genes encoding bile acid altering enzymes were able to impact how B. theta responds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci (PULs). This suggests that B. theta may be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut. This work will aid in our understanding of how to rationally manipulate the bile acid pool and the microbiota to exploit carbohydrate metabolism in the context of inflammation and other GI diseases.
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Affiliation(s)
- Arthur S. McMillan
- Genetics Program, Department of Biological Sciences, College of Science
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Matthew H. Foley
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Caroline E. Perkins
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
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Corrêa RO, Castro PR, Fachi JL, Nirello VD, El-Sahhar S, Imada S, Pereira GV, Pral LP, Araújo NVP, Fernandes MF, Matheus VA, de Souza Felipe J, Dos Santos Pereira Gomes AB, de Oliveira S, de Rezende Rodovalho V, de Oliveira SRM, de Assis HC, Oliveira SC, Dos Santos Martins F, Martens E, Colonna M, Varga-Weisz P, Vinolo MAR. Inulin diet uncovers complex diet-microbiota-immune cell interactions remodeling the gut epithelium. MICROBIOME 2023; 11:90. [PMID: 37101209 PMCID: PMC10131329 DOI: 10.1186/s40168-023-01520-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND The continuous proliferation of intestinal stem cells followed by their tightly regulated differentiation to epithelial cells is essential for the maintenance of the gut epithelial barrier and its functions. How these processes are tuned by diet and gut microbiome is an important, but poorly understood question. Dietary soluble fibers, such as inulin, are known for their ability to impact the gut bacterial community and gut epithelium, and their consumption has been usually associated with health improvement in mice and humans. In this study, we tested the hypothesis that inulin consumption modifies the composition of colonic bacteria and this impacts intestinal stem cells functions, thus affecting the epithelial structure. METHODS Mice were fed with a diet containing 5% of the insoluble fiber cellulose or the same diet enriched with an additional 10% of inulin. Using a combination of histochemistry, host cell transcriptomics, 16S microbiome analysis, germ-free, gnotobiotic, and genetically modified mouse models, we analyzed the impact of inulin intake on the colonic epithelium, intestinal bacteria, and the local immune compartment. RESULTS We show that the consumption of inulin diet alters the colon epithelium by increasing the proliferation of intestinal stem cells, leading to deeper crypts and longer colons. This effect was dependent on the inulin-altered gut microbiota, as no modulations were observed in animals deprived of microbiota, nor in mice fed cellulose-enriched diets. We also describe the pivotal role of γδ T lymphocytes and IL-22 in this microenvironment, as the inulin diet failed to induce epithelium remodeling in mice lacking this T cell population or cytokine, highlighting their importance in the diet-microbiota-epithelium-immune system crosstalk. CONCLUSION This study indicates that the intake of inulin affects the activity of intestinal stem cells and drives a homeostatic remodeling of the colon epithelium, an effect that requires the gut microbiota, γδ T cells, and the presence of IL-22. Our study indicates complex cross kingdom and cross cell type interactions involved in the adaptation of the colon epithelium to the luminal environment in steady state. Video Abstract.
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Affiliation(s)
- Renan Oliveira Corrêa
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02139, USA.
| | - Pollyana Ribeiro Castro
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - José Luís Fachi
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Vinícius Dias Nirello
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Salma El-Sahhar
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Shinya Imada
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02139, USA
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Gabriel Vasconcelos Pereira
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laís Passariello Pral
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Nathália Vitoria Pereira Araújo
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Mariane Font Fernandes
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Valquíria Aparecida Matheus
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Jaqueline de Souza Felipe
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Arilson Bernardo Dos Santos Pereira Gomes
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Sarah de Oliveira
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Vinícius de Rezende Rodovalho
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Samantha Roberta Machado de Oliveira
- Laboratory of Biotherapeutics Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Helder Carvalho de Assis
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Sergio Costa Oliveira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Flaviano Dos Santos Martins
- Laboratory of Biotherapeutics Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Eric Martens
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Patrick Varga-Weisz
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- São Paulo Excellence Chair, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Marco Aurélio Ramirez Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil.
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil.
- Experimental Medicine Research Cluster, Campinas, SP, 13083-862, Brazil.
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, SP, 13083-864, Brazil.
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Gut microbiota alters host bile acid metabolism to contribute to intrahepatic cholestasis of pregnancy. Nat Commun 2023; 14:1305. [PMID: 36894566 PMCID: PMC9998625 DOI: 10.1038/s41467-023-36981-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Intrahepatic cholestasis of pregnancy (ICP) is a female pregnancy-specific disorder that is characterized by increased serum bile acid and adverse fetal outcomes. The aetiology and mechanism of ICP are poorly understood; thus, existing therapies have been largely empiric. Here we show that the gut microbiome differed significantly between individuals with ICP and healthy pregnant women, and that colonization with gut microbiome from ICP patients was sufficient to induce cholestasis in mice. The gut microbiomes of ICP patients were primarily characterized by Bacteroides fragilis (B. fragilis), and B. fragilis was able to promote ICP by inhibiting FXR signaling via its BSH activity to modulate bile acid metabolism. B. fragilis-mediated FXR signaling inhibition was responsible for excessive bile acid synthesis and interrupted hepatic bile excretion to ultimately promote the initiation of ICP. We propose that modulation of the gut microbiota-bile acid-FXR axis may be of value for ICP treatment.
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Song P, Zhang X, Feng W, Xu W, Wu C, Xie S, Yu S, Fu R. Biological synthesis of ursodeoxycholic acid. Front Microbiol 2023; 14:1140662. [PMID: 36910199 PMCID: PMC9998936 DOI: 10.3389/fmicb.2023.1140662] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/13/2023] [Indexed: 03/14/2023] Open
Abstract
Ursodeoxycholic acid (UDCA) is a fundamental treatment drug for numerous hepatobiliary diseases that also has adjuvant therapeutic effects on certain cancers and neurological diseases. Chemical UDCA synthesis is environmentally unfriendly with low yields. Biological UDCA synthesis by free-enzyme catalysis or whole-cell synthesis using inexpensive and readily available chenodeoxycholic acid (CDCA), cholic acid (CA), or lithocholic acid (LCA) as substrates is being developed. The free enzyme-catalyzed one-pot, one-step/two-step method uses hydroxysteroid dehydrogenase (HSDH); whole-cell synthesis, mainly uses engineered bacteria (mainly Escherichia coli) expressing the relevant HSDHs. To further develop these methods, HSDHs with specific coenzyme dependence, high enzyme activity, good stability, and high substrate loading concentration, P450 monooxygenase with C-7 hydroxylation activity and engineered strain harboring HSDHs must be exploited.
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Affiliation(s)
- Peng Song
- College of Life Sciences, Liaocheng University, Liaocheng, China
- Jiangxi Zymerck Biotechnology Co., Ltd., Nanchang, China
| | - Xue Zhang
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Wei Feng
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Wei Xu
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Chaoyun Wu
- Jiangxi Zymerck Biotechnology Co., Ltd., Nanchang, China
| | - Shaoqing Xie
- Jiangxi Zymerck Biotechnology Co., Ltd., Nanchang, China
| | - Sisi Yu
- Jiangxi Zymerck Biotechnology Co., Ltd., Nanchang, China
| | - Rongzhao Fu
- Jiangxi Zymerck Biotechnology Co., Ltd., Nanchang, China
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A Novel NADP(H)-Dependent 7alpha-HSDH: Discovery and Construction of Substrate Selectivity Mutant by C-Terminal Truncation. Catalysts 2022. [DOI: 10.3390/catal12070781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
7α-Hydroxysteroid dehydrogenase (7α-HSDH) plays an important role in the biosynthesis of tauroursodeoxycholic acid (TUDCA) using complex substrate chicken bile powder as raw material. However, chicken bile powder contains 4.74% taurocholic acid (TCA), and a new by-product tauroursocholic acid (TUCA) will be produced, having the risk of causing colorectal cancer. Here, we obtained a novel NADP(H)-dependent 7α-HSDH with good thermostability from Ursus thibetanus gut microbiota (named St-2-2). St-2-2 could catalyze taurochenodeoxycholic acid (TCDCA) and TCA with the catalytic activity of 128.13 and 269.39 U/mg, respectively. Interestingly, by a structure-based C-terminal truncation strategy, St-2-2△C10 only remained catalytic activity on TCDCA (14.19 U/mg) and had no activity on TCA. As a result, it can selectively catalyze TCDCA in waste chicken bile powder. MD simulation and structural analysis indicated that enhanced surface hydrophilicity and improved C-terminal rigidity affected the entry and exit of substrates. Hydrogen bond interactions between different subunits and interaction changes in Phe249 of the C-terminal loop inverted the substrate catalytic activity. This is the first report on substrate selectivity of 7α-HSDH by C-terminal truncation strategy and it can be extended to other 7α-HSDHs (J-1-1, S1-a-1).
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9
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Favale N, Costa S, Scapoli C, Carrieri A, Sabbioni S, Tamburini E, Benazzo A, Bernacchia G. Reconstruction of Acinetobacter johnsonii ICE_NC genome using hybrid de novo genome assemblies and identification of the 12α-hydroxysteroid dehydrogenase gene. J Appl Microbiol 2022; 133:1506-1519. [PMID: 35686660 PMCID: PMC9540589 DOI: 10.1111/jam.15657] [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: 02/25/2022] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022]
Abstract
AIMS The role of a Acinetobacter johnsonii strain, isolated from a soil sample, in the biotransformation of bile acids (BAs) was already described but the enzymes responsible for these transformations were only partially purified and molecularly characterized. METHODS AND RESULTS This study describes the use of hybrid de novo assemblies, that combine long-read Oxford Nanopore and short-read Illumina sequencing strategies, to reconstruct the entire genome of A. johnsonii ICE_NC strain and to identify the coding region for a 12α-hydroxysteroid dehydrogenase (12α-HSDH), involved in BAs metabolism. The de novo assembly of the A. johnsonii ICE_NC genome was generated using Canu and Unicycler, both strategies yielded a circular chromosome of about 3.6 Mb and one 117 kb long plasmid. Gene annotation was performed on the final assemblies and the gene for 12α-HSDH was detected on the plasmid. CONCLUSIONS Our findings illustrate the added value of long read sequencing in addressing the challenges of whole genome characterization and plasmid reconstruction in bacteria. These approaches also allowed the identification of the A. johnsonii ICE_NC gene for the 12α-HSDH enzyme, whose activity was confirmed at the biochemical level. SIGNIFICANCE AND IMPACT OR THE STUDY At present, this is the first report on the characterization of a 12α-HSDH gene in an A. johnsonii strain able to biotransform cholic acid into ursodeoxycholic acid, a promising therapeutic agent for several diseases.
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Affiliation(s)
- Nicoletta Favale
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Stefania Costa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.,Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alberto Carrieri
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Sabbioni
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Elena Tamburini
- Department of Environmental Sciences and Prevention, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giovanni Bernacchia
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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10
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Liu L, Zhang J, Cheng Y, Zhu M, Xiao Z, Ruan G, Wei Y. Gut microbiota: A new target for T2DM prevention and treatment. Front Endocrinol (Lausanne) 2022; 13:958218. [PMID: 36034447 PMCID: PMC9402911 DOI: 10.3389/fendo.2022.958218] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM), one of the fastest growing metabolic diseases, has been characterized by metabolic disorders including hyperglycemia, hyperlipidemia and insulin resistance (IR). In recent years, T2DM has become the fastest growing metabolic disease in the world. Studies have indicated that patients with T2DM are often associated with intestinal flora disorders and dysfunction involving multiple organs. Metabolites of the intestinal flora, such as bile acids (BAs), short-chain fatty acids (SCFAs) and amino acids (AAs)may influence to some extent the decreased insulin sensitivity associated with T2DM dysfunction and regulate metabolic as well as immune homeostasis. In this paper, we review the changes in the gut flora in T2DM and the mechanisms by which the gut microbiota modulates metabolites affecting T2DM, which may provide a basis for the early identification of T2DM-susceptible individuals and guide targeted interventions. Finally, we also highlight gut microecological therapeutic strategies focused on shaping the gut flora to inform the improvement of T2DM progression.
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Affiliation(s)
- Lulu Liu
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jiheng Zhang
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yi Cheng
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Meng Zhu
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhifeng Xiao
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Guangcong Ruan
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Yanling Wei, ; Guangcong Ruan,
| | - Yanling Wei
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Yanling Wei, ; Guangcong Ruan,
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11
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Kim KH, Lee CW, Pardhe BD, Hwang J, Do H, Lee YM, Lee JH, Oh TJ. Crystal structure of an apo 7α-hydroxysteroid dehydrogenase reveals key structural changes induced by substrate and co-factor binding. J Steroid Biochem Mol Biol 2021; 212:105945. [PMID: 34171491 DOI: 10.1016/j.jsbmb.2021.105945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 11/23/2022]
Abstract
7α-Hydroxysteroid dehydrogenase (7α-HSDH) catalyzes the dehydrogenation of a hydroxyl group at the 7α position in steroid substrates using NAD+ or NADP+ as a co-factor. Although studies have determined the binary and ternary complex structures, detailed structural changes induced by ligand and co-factor binding remain unclear, because ligand-free structures are not yet available. Here, we present the crystal structure of apo 7α-HSDH from Escherichia coli (Eco-7α-HSDH) at 2.7 Å resolution. We found that the apo form undergoes substantial conformational changes in the β4-α4 loop, α7-α8 helices, and C-terminus loop among the four subunits comprising the tetramer. Furthermore, a comparison of the apo structure with the binary (NAD+)-complex and ternary (NADH and 7-oxoglycochenodeoxycholic acid)-complex Eco-7α-HSDH structures revealed that only the ternary-complex structure has a fully closed conformation, whereas the binary-complex and apo structures have a semi-closed or open conformation. This open-to-closed transition forces several catalytically important residues (S146, Y159, and K163) into correct positions for catalysis. To confirm the catalytic activity, we used alcohol dehydrogenase for NAD+ regeneration to allow efficient conversion of chenodeoxycholic acid to 7-ketolithocholic acid by Eco-7α-HSDH. These findings demonstrate that apo Eco-7α-HSDH exhibits intrinsically flexible characteristics with an open conformation. This structural information provides novel insight into the 7α-HSDH reaction mechanism.
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Affiliation(s)
- Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea
| | - Chang Woo Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea; Genome-based BioIT Convergence Institute, Asan, 31460, Republic of Korea; Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, Republic of Korea.
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12
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Lou D, Liu X, Tan J. An Overview of 7α- and 7β-Hydroxysteroid Dehydrogenases: Structure, Specificity and Practical Application. Protein Pept Lett 2021; 28:1206-1219. [PMID: 34397319 DOI: 10.2174/0929866528666210816114032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 05/27/2021] [Accepted: 06/17/2021] [Indexed: 11/22/2022]
Abstract
7α-Hydroxysteroid dehydrogenase and 7β-hydroxysteroid dehydrogenase are key enzymes involved in bile acid metabolism. They catalyze the epimerization of a hydroxyl group through 7-keto bile acid intermediates. Basic research of the two enzymes has focused on exploring new enzymes and the structure-function relationship. The application research focused on the in vitro biosynthesis of bile acid drugs and the exploration and improvement of their catalytic ability based on molecular engineering. This article summarized the primary and advanced structural characteristics, specificities, biochemical properties, and applications of the two enzymes. The emphasis is also given to obtaining of novel 7α-hydroxysteroid dehydrogenase and 7β-hydroxysteroid dehydrogenase that are thermally stable and active in the presence of organic solvents, high substrate concentration, and extreme pH values. To achieve these goals, enzyme redesigning based on protein engineering and genomics may be the most useful approaches.
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Affiliation(s)
- Deshuai Lou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China
| | - Xi Liu
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China
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13
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Liu Z, Zhang R, Zhang W, Xu Y. Ile258Met mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase significantly enhances catalytic efficiency, cofactor affinity, and thermostability. Appl Microbiol Biotechnol 2021; 105:3573-3586. [PMID: 33937927 DOI: 10.1007/s00253-021-11299-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/25/2021] [Accepted: 04/17/2021] [Indexed: 12/20/2022]
Abstract
NAD(H)-dependent 7α-hydroxysteroid dehydrogenase catalyzes the oxidation of chenodeoxycholic acid to 7-oxolithocholic acid. Here, we designed mutations of Ile258 adjacent to the catalytic pocket of Brucella melitensis 7α-hydroxysteroid dehydrogenase. The I258M variant gave a 4.7-fold higher kcat, but 4.5-fold lower KM, compared with the wild type, resulting in a 21.8-fold higher kcat/KM value for chenodeoxycholic acid oxidation. It presented a 2.0-fold lower KM value with NAD+, suggesting stronger binding to the cofactor. I258M produced 7-oxolithocholic acid in the highest yield of 92.3% in 2 h, whereas the wild-type gave 88.4% in 12 h. The I258M mutation increased the half-life from 20.8 to 31.1 h at 30 °C. Molecular dynamics simulations indicated increased interactions and a modified tunnel improved the catalytic efficiency, and enhanced rigidity at three regions around the ligand-binding pocket increased the enzyme thermostability. This is the first report about significantly improved catalytic efficiency, cofactor affinity, and enzyme thermostability through single site-mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase. KEY POINTS: • Sequence and structure analysis guided the site mutation design. • Thermostability, catalytic efficiency and 7-oxo-LCA production were determined. • MD simulation was performed to indicate the improvement by I258M mutation.
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Affiliation(s)
- Zhiyong Liu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China.
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
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14
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Microbial Hydroxysteroid Dehydrogenases: From Alpha to Omega. Microorganisms 2021; 9:microorganisms9030469. [PMID: 33668351 PMCID: PMC7996314 DOI: 10.3390/microorganisms9030469] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 12/23/2022] Open
Abstract
Bile acids (BAs) and glucocorticoids are steroid hormones derived from cholesterol that are important signaling molecules in humans and other vertebrates. Hydroxysteroid dehydrogenases (HSDHs) are encoded both by the host and by their resident gut microbiota, and they reversibly convert steroid hydroxyl groups to keto groups. Pairs of HSDHs can reversibly epimerize steroids from α-hydroxy conformations to β-hydroxy, or β-hydroxy to ω-hydroxy in the case of ω-muricholic acid. These reactions often result in products with drastically different physicochemical properties than their precursors, which can result in steroids being activators or inhibitors of host receptors, can affect solubility in fecal water, and can modulate toxicity. Microbial HSDHs modulate sterols associated with diseases such as colorectal cancer, liver cancer, prostate cancer, and polycystic ovary syndrome. Although the role of microbial HSDHs is not yet fully elucidated, they may have therapeutic potential as steroid pool modulators or druggable targets in the future. In this review, we explore metabolism of BAs and glucocorticoids with a focus on biotransformation by microbial HSDHs.
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15
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Jia W, Wei M, Rajani C, Zheng X. Targeting the alternative bile acid synthetic pathway for metabolic diseases. Protein Cell 2020; 12:411-425. [PMID: 33252713 PMCID: PMC8106556 DOI: 10.1007/s13238-020-00804-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is profoundly involved in glucose and lipid metabolism, in part by regulating bile acid (BA) metabolism and affecting multiple BA-receptor signaling pathways. BAs are synthesized in the liver by multi-step reactions catalyzed via two distinct routes, the classical pathway (producing the 12α-hydroxylated primary BA, cholic acid), and the alternative pathway (producing the non-12α-hydroxylated primary BA, chenodeoxycholic acid). BA synthesis and excretion is a major pathway of cholesterol and lipid catabolism, and thus, is implicated in a variety of metabolic diseases including obesity, insulin resistance, and nonalcoholic fatty liver disease. Additionally, both oxysterols and BAs function as signaling molecules that activate multiple nuclear and membrane receptor-mediated signaling pathways in various tissues, regulating glucose, lipid homeostasis, inflammation, and energy expenditure. Modulating BA synthesis and composition to regulate BA signaling is an interesting and novel direction for developing therapies for metabolic disease. In this review, we summarize the most recent findings on the role of BA synthetic pathways, with a focus on the role of the alternative pathway, which has been under-investigated, in treating hyperglycemia and fatty liver disease. We also discuss future perspectives to develop promising pharmacological strategies targeting the alternative BA synthetic pathway for the treatment of metabolic diseases.
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Affiliation(s)
- Wei Jia
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China. .,School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - Meilin Wei
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Cynthia Rajani
- University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Xiaojiao Zheng
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
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16
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Abstract
Vertebrates synthesize a diverse set of steroids and bile acids that undergo bacterial biotransformations. The endocrine literature has principally focused on the biochemistry and molecular biology of host synthesis and tissue-specific metabolism of steroids. Host-associated microbiota possess a coevolved set of steroid and bile acid modifying enzymes that match the majority of host peripheral biotransformations in addition to unique capabilities. The set of host-associated microbial genes encoding enzymes involved in steroid transformations is known as the sterolbiome. This review focuses on the current knowledge of the sterolbiome as well as its importance in medicine and agriculture.
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17
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Ferrandi EE, Bertuletti S, Monti D, Riva S. Hydroxysteroid Dehydrogenases: An Ongoing Story. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000192] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Erica Elisa Ferrandi
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC); Consiglio Nazionale delle Ricerche (CNR); Via Mario Bianco 9 20131 Milano Italy
| | - Susanna Bertuletti
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC); Consiglio Nazionale delle Ricerche (CNR); Via Mario Bianco 9 20131 Milano Italy
- Università degli Studi di Milano; Via Giuseppe Colombo 60 20133 Milano Italy
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC); Consiglio Nazionale delle Ricerche (CNR); Via Mario Bianco 9 20131 Milano Italy
| | - Sergio Riva
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC); Consiglio Nazionale delle Ricerche (CNR); Via Mario Bianco 9 20131 Milano Italy
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18
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Shi S, You Z, Zhou K, Chen Q, Pan J, Qian X, Xu J, Li C. Efficient Synthesis of 12‐Oxochenodeoxycholic Acid Using a 12α‐Hydroxysteroid Dehydrogenase fromRhodococcus ruber. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900849] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shou‐Cheng Shi
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Zhi‐Neng You
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Ke Zhou
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Qi Chen
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing, School of BiotechnologyEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Jiang Pan
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing, School of BiotechnologyEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Xiao‐Long Qian
- Suzhou Bioforany EnzyTech Co. Ltd. No. 8 Yanjiuyuan Road, Economic Development Zone, Changshu Jiangsu 215512 People's Republic of China
| | - Jian‐He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing, School of BiotechnologyEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Chun‐Xiu Li
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing, School of BiotechnologyEast China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
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19
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Zhang X, Fan D, Hua X, Zhang T. Large-scale production of ursodeoxycholic acid from chenodeoxycholic acid by engineering 7α- and 7β-hydroxysteroid dehydrogenase. Bioprocess Biosyst Eng 2019; 42:1537-1545. [DOI: 10.1007/s00449-019-02151-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 05/11/2019] [Indexed: 10/26/2022]
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20
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Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. MICROBIOME 2019; 7:75. [PMID: 31092280 PMCID: PMC6521386 DOI: 10.1186/s40168-019-0689-3] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/26/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities. RESULTS Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life ). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model. CONCLUSIONS This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Dmitry A Ravcheev
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Federico Baldini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Laurent Heirendt
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ronan M T Fleming
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden, Leiden, The Netherlands
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland.
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21
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Tang S, Pan Y, Lou D, Ji S, Zhu L, Tan J, Qi N, Yang Q, Zhang Z, Yang B, Zhao W, Wang B. Structural and functional characterization of a novel acidophilic 7α-hydroxysteroid dehydrogenase. Protein Sci 2019; 28:910-919. [PMID: 30839141 PMCID: PMC6460000 DOI: 10.1002/pro.3599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/09/2022]
Abstract
7α-Hydroxysteroid dehydrogenase (7α-HSDH) is an NAD(P)H-dependent oxidoreductase belonging to the short-chain dehydrogenases/reductases. In vitro, 7α-HSDH is involved in the efficient biotransformation of taurochenodeoxycholic acid (TCDCA) to tauroursodeoxycholic acid (TUDCA). In this study, a gene encoding novel 7α-HSDH (named as St-2-1) from fecal samples of black bear was cloned and heterologously expressed in Escherichia coli. The protein has subunits of 28.3 kDa and a native size of 56.6 kDa, which suggested a homodimer. We studied the relevant properties of the enzyme, including the optimum pH, optimum temperature, thermal stability, activators, and inhibitors. Interestingly, the data showed that St-2-1 differs from the 7α-HSDHs reported in the literature, as it functions under acidic conditions. The enzyme displayed its optimal activity at pH 5.5 (TCDCA). The acidophilic nature of 7α-HSDH expands its application environment and the natural enzyme bank of HSDHs, providing a promising candidate enzyme for the biosynthesis of TUDCA or other related chemical entities.
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Affiliation(s)
- Shijin Tang
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Yinping Pan
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Deshuai Lou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir RegionSchool of Biological & Chemical Engineering, Chongqing University of EducationChongqing 400067China
| | - Shunlin Ji
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
- Modern Life Science Experiment Teaching CenterCollege of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir RegionSchool of Biological & Chemical Engineering, Chongqing University of EducationChongqing 400067China
| | - Na Qi
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Qiong Yang
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
- Chongqing Key Laboratory of Inorganic Special Functional MaterialsCollaborative Innovation Center for Green Development in Wuling Mountain Areas, Yangtze Normal UniversityChongqing 408100China
| | - Zhi Zhang
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Biling Yang
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Wenyan Zhao
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and TechnologyMinistry of Education, College of Bioengineering, Chongqing UniversityChongqing 400030China
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22
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Ding Y, Yanagi K, Cheng C, Alaniz RC, Lee K, Jayaraman A. Interactions between gut microbiota and non-alcoholic liver disease: The role of microbiota-derived metabolites. Pharmacol Res 2019; 141:521-529. [PMID: 30660825 PMCID: PMC6392453 DOI: 10.1016/j.phrs.2019.01.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023]
Abstract
There is increasing evidence that the intestinal microbiota plays a mechanistic role in the etiology of non-alcoholic fatty liver disease (NAFLD). Animal and human studies have linked small molecule metabolites produced by commensal bacteria in the gut contribute to not only intestinal inflammation, but also to hepatic inflammation. These immunomodulatory metabolites are capable of engaging host cellular receptors, and may mediate the observed association between gut dysbiosis and NAFLD. This review focuses on the effects and potential mechanisms of three specific classes of metabolites that synthesized or modified by gut bacteria: short chain fatty acids, amino acid catabolites, and bile acids. In particular, we discuss their role as ligands for cell surface and nuclear receptors regulating metabolic and inflammatory pathways in the intestine and liver. Studies reveal that the metabolites can both agonize and antagonize their cognate receptors to reduce or exacerbate liver steatosis and inflammation, and that the effects are metabolite- and context-specific. Further studies are warranted to more comprehensively understand bacterial metabolite-mediated gut-liver in NAFLD. This understanding could help identify novel therapeutics and therapeutic targets to intervene in the disease through the gut microbiota.
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Affiliation(s)
- Yufang Ding
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Karin Yanagi
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Clint Cheng
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA
| | - Robert C Alaniz
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA.
| | - Arul Jayaraman
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843, USA.
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Enhanced activity and substrate tolerance of 7α-hydroxysteroid dehydrogenase by directed evolution for 7-ketolithocholic acid production. Appl Microbiol Biotechnol 2019; 103:2665-2674. [PMID: 30734123 DOI: 10.1007/s00253-019-09668-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/20/2018] [Accepted: 01/27/2019] [Indexed: 01/14/2023]
Abstract
7-Ketolithocholic acid (7-KLCA) is an important intermediate for the synthesis of ursodeoxycholic acid (UDCA). UDCA is the main effective component of bear bile powder that is used in traditional Chinese medicine for the treatment of human cholesterol gallstones. 7α-Hydroxysteroid dehydrogenase (7α-HSDH) is the key enzyme used in the industrial production of 7-KLCA. Unfortunately, the natural 7α-HSDHs reported have difficulty meeting the requirements of industrial application, due to their poor activities and strong substrate inhibition. In this study, a directed evolution strategy combined with high-throughput screening was applied to improve the catalytic efficiency and tolerance of high substrate concentrations of NADP+-dependent 7α-HSDH from Clostridium absonum. Compared with the wild type, the best mutant (7α-3) showed 5.5-fold higher specific activity and exhibited 10-fold higher and 14-fold higher catalytic efficiency toward chenodeoxycholic acid (CDCA) and NADP+, respectively. Moreover, 7α-3 also displayed significantly enhanced tolerance in the presence of high concentrations of substrate compared to the wild type. Owing to its improved catalytic efficiency and enhanced substrate tolerance, 7α-3 could efficiently biosynthesize 7-KLCA with a substrate loading of 100 mM, resulting in 99% yield of 7-KLCA at 2 h, in contrast to only 85% yield of 7-KLCA achieved for the wild type at 16 h.
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24
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Ji Q, Wang B, Li C, Hao J, Feng W. Co-immobilised 7α- and 7β-HSDH as recyclable biocatalyst: high-performance production of TUDCA from waste chicken bile. RSC Adv 2018; 8:34192-34201. [PMID: 35548603 PMCID: PMC9086975 DOI: 10.1039/c8ra06798h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/26/2018] [Indexed: 11/21/2022] Open
Abstract
Chicken gallbladder has long been considered to be worthless and discarded as waste. The main composition of chicken bile is taurochenodeoxycholic acid (TCDCA), which is the isomeride of tauroursodeoxycholic acid (TUDCA). TUDCA has been effectively used for treatment of many diseases. In this paper, 7α- and 7β-hydroxysteroid dehydrogenases (HSDH) were co-immobilised on modified chitosan microspheres, and used as recyclable biocatalyst for the catalysis of chicken bile. The catalytic reaction reached equilibrium within 4 h compared with 1 h using TCDCA as substrate. After four continuous batch reactions, the conversion of TCDCA was lower than 40% and TUDCA yield was about 15% for the catalysis of chicken bile. TUDCA yield was approximately 62% after equilibrium and the content of TUDCA in reaction product was as high as 33.16%. Furthermore, the experiments showed that activity of enzymes were significantly inhibited by bilirubin, Cu2+ and Ca2+ in complex substrate. The research described not only widens the utilization of chicken bile, but also provides a clean way for the preparation of TUDCA.
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Affiliation(s)
- Qingzhi Ji
- School of Pharmacy, Yancheng Teachers' University No. 2, Hope Avenue Yancheng Jiangsu 224051 P. R. China +86-0515-88258773 +86-0515-88258773
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University Chongqing 400030 P. R. China
| | - Chou Li
- College of Marine and Bio-engineering, Yancheng Teachers' University Yancheng Jiangsu 224051 P. R. China
| | - Jinglan Hao
- School of Pharmacy, Yancheng Teachers' University No. 2, Hope Avenue Yancheng Jiangsu 224051 P. R. China +86-0515-88258773 +86-0515-88258773
| | - Wenjing Feng
- School of Pharmacy, Yancheng Teachers' University No. 2, Hope Avenue Yancheng Jiangsu 224051 P. R. China +86-0515-88258773 +86-0515-88258773
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25
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Harris SC, Devendran S, Méndez- García C, Mythen SM, Wright CL, Fields CJ, Hernandez AG, Cann I, Hylemon PB, Ridlon JM. Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243 T. Gut Microbes 2018; 9:523-539. [PMID: 29617190 PMCID: PMC6287680 DOI: 10.1080/19490976.2018.1458180] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Strains of Eggerthella lenta are capable of oxidation-reduction reactions capable of oxidizing and epimerizing bile acid hydroxyl groups. Several genes encoding these enzymes, known as hydroxysteroid dehydrogenases (HSDH) have yet to be identified. It is also uncertain whether the products of E. lenta bile acid metabolism are further metabolized by other members of the gut microbiota. We characterized a novel human fecal isolate identified as E. lenta strain C592. The complete genome of E. lenta strain C592 was sequenced and comparative genomics with the type strain (DSM 2243) revealed high conservation, but some notable differences. E. lenta strain C592 falls into group III, possessing 3α, 3β, 7α, and 12α-hydroxysteroid dehydrogenase (HSDH) activity, as determined by mass spectrometry of thin layer chromatography (TLC) separated metabolites of primary and secondary bile acids. Incubation of E. lenta oxo-bile acid and iso-bile acid metabolites with whole-cells of the high-activity bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI 12708, resulted in minimal conversion of oxo-derivatives to lithocholic acid (LCA). Further, Iso-chenodeoxycholic acid (iso-CDCA; 3β,7α-dihydroxy-5β-cholan-24-oic acid) was not metabolized by C. scindens. We then located a gene encoding a novel 12α-HSDH in E. lenta DSM 2243, also encoded by strain C592, and the recombinant purified enzyme was characterized and substrate-specificity determined. Genomic analysis revealed genes encoding an Rnf complex (rnfABCDEG), an energy conserving hydrogenase (echABCDEF) complex, as well as what appears to be a complete Wood-Ljungdahl pathway. Our prediction that by changing the gas atmosphere from nitrogen to hydrogen, bile acid oxidation would be inhibited, was confirmed. These results suggest that E. lenta is an important bile acid metabolizing gut microbe and that the gas atmosphere may be an important and overlooked regulator of bile acid metabolism in the gut.
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Affiliation(s)
- Spencer C. Harris
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,McGuire Veterans Affairs, Richmond, VA, USA
| | - Saravanan Devendran
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Sean M. Mythen
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chris L. Wright
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J. Fields
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alvaro G. Hernandez
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,McGuire Veterans Affairs, Richmond, VA, USA
| | - Jason M. Ridlon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA,CONTACT Jason M. Ridlon Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL USA
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26
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Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12α-Hydroxysteroid Dehydrogenases from Bile Acid 7α-Dehydroxylating Human Gut Bacteria. Appl Environ Microbiol 2018; 84:AEM.00235-18. [PMID: 29549099 DOI: 10.1128/aem.00235-18] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
Bile acids are important cholesterol-derived nutrient signaling hormones, synthesized in the liver, that act as detergents to solubilize dietary lipids. Bile acid 7α-dehydroxylating gut bacteria generate the toxic bile acids deoxycholic acid and lithocholic acid from host bile acids. The ability of these bacteria to remove the 7-hydroxyl group is partially dependent on 7α-hydroxysteroid dehydrogenase (HSDH) activity, which reduces 7-oxo-bile acids generated by other gut bacteria. 3α-HSDH has an important enzymatic activity in the bile acid 7α-dehydroxylation pathway. 12α-HSDH activity has been reported for the low-activity bile acid 7α-dehydroxylating bacterium Clostridium leptum; however, this activity has not been reported for high-activity bile acid 7α-dehydroxylating bacteria, such as Clostridium scindens, Clostridium hylemonae, and Clostridium hiranonis Here, we demonstrate that these strains express bile acid 12α-HSDH. The recombinant enzymes were characterized from each species and shown to preferentially reduce 12-oxolithocholic acid to deoxycholic acid, with low activity against 12-oxochenodeoxycholic acid and reduced activity when bile acids were conjugated to taurine or glycine. Phylogenetic analysis suggests that 12α-HSDH is widespread among Firmicutes, Actinobacteria in the Coriobacteriaceae family, and human gut ArchaeaIMPORTANCE 12α-HSDH activity has been established in the medically important bile acid 7α-dehydroxylating bacteria C. scindens, C. hiranonis, and C. hylemonae Experiments with recombinant 12α-HSDHs from these strains are consistent with culture-based experiments that show a robust preference for 12-oxolithocholic acid over 12-oxochenodeoxycholic acid. Phylogenetic analysis identified novel members of the gut microbiome encoding 12α-HSDH. Future reengineering of 12α-HSDH enzymes to preferentially oxidize cholic acid may provide a means to industrially produce the therapeutic bile acid ursodeoxycholic acid. In addition, a cholic acid-specific 12α-HSDH expressed in the gut may be useful for the reduction in deoxycholic acid concentration, a bile acid implicated in cancers of the gastrointestinal (GI) tract.
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27
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Tonin F, Arends IWCE. Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review. Beilstein J Org Chem 2018; 14:470-483. [PMID: 29520309 PMCID: PMC5827811 DOI: 10.3762/bjoc.14.33] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/05/2018] [Indexed: 12/13/2022] Open
Abstract
Ursodeoxycholic acid (UDCA) is a pharmaceutical ingredient widely used in clinics. As bile acid it solubilizes cholesterol gallstones and improves the liver function in case of cholestatic diseases. UDCA can be obtained from cholic acid (CA), which is the most abundant and least expensive bile acid available. The now available chemical routes for the obtainment of UDCA yield about 30% of final product. For these syntheses several protection and deprotection steps requiring toxic and dangerous reagents have to be performed, leading to the production of a series of waste products. In many cases the cholic acid itself first needs to be prepared from its taurinated and glycilated derivatives in the bile, thus adding to the complexity and multitude of steps involved of the synthetic process. For these reasons, several studies have been performed towards the development of microbial transformations or chemoenzymatic procedures for the synthesis of UDCA starting from CA or chenodeoxycholic acid (CDCA). This promising approach led several research groups to focus their attention on the development of biotransformations with non-pathogenic, easy-to-manage microorganisms, and their enzymes. In particular, the enzymatic reactions involved are selective hydrolysis, epimerization of the hydroxy functions (by oxidation and subsequent reduction) and the specific hydroxylation and dehydroxylation of suitable positions in the steroid rings. In this minireview, we critically analyze the state of the art of the production of UDCA by several chemical, chemoenzymatic and enzymatic routes reported, highlighting the bottlenecks of each production step. Particular attention is placed on the precursors availability as well as the substrate loading in the process. Potential new routes and recent developments are discussed, in particular on the employment of flow-reactors. The latter technology allows to develop processes with shorter reaction times and lower costs for the chemical and enzymatic reactions involved.
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Affiliation(s)
- Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Isabel W C E Arends
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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28
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Lou D, Wang Y, Tan J, Zhu L, Ji S, Wang B. Functional contribution of coenzyme specificity-determining sites of 7α-hydroxysteroid dehydrogenase from Clostridium absonum. Comput Biol Chem 2017; 70:89-95. [PMID: 28826103 DOI: 10.1016/j.compbiolchem.2017.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 05/25/2017] [Accepted: 08/06/2017] [Indexed: 10/19/2022]
Abstract
Studies of the molecular determinants of coenzyme specificity help to reveal the structure-function relationship of enzymes, especially with regards to coenzyme specificity-determining sites (CSDSs) that usually mediate complex interactions. NADP(H)-dependent 7α-hydroxysteroid dehydrogenase from Clostridium absonum (CA 7α-HSDH), a member of the short-chain dehydrogenase/reductase superfamily (SDRs), possesses positively charged CSDSs that mainly contain T15, R16, R38, and R194, forming complicated polar interactions with the adenosine ribose C2 phosphate group of NADP(H). The R38 residue is crucial for coenzyme anchoring, but the influence of the other residues on coenzyme utilization is still not clear. Hence, we performed alanine scanning mutagenesis and molecular dynamic (MD) simulations. The results suggest that the natural CSDSs have the greatest NADP(H)-binding affinity, but not the best activity (kcat) toward NADP+. Compared with the wild type and other mutants, the mutant R194A showed the highest catalytic efficiency (kcat/Km), which was more than three-times that of the wild type. MD simulation and kinetics analysis suggested that the importance of the CSDSs of CA 7α-HSDH should be in accordance with the following order R38>T15>R16>R194, and S39 may have a supporting role in NADP(H) anchoring for mutants R16A/T194A and T15A/R16A/T194A.
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Affiliation(s)
- Deshuai Lou
- Postdoctoral Research Station of Biology, Chongqing University, Chongqing 400030, China; Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Yue Wang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological & Chemical engineering, Chongqing University of Education, Chongqing 400067, China.
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Shunlin Ji
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China.
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Long SL, Gahan CGM, Joyce SA. Interactions between gut bacteria and bile in health and disease. Mol Aspects Med 2017; 56:54-65. [PMID: 28602676 DOI: 10.1016/j.mam.2017.06.002] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/26/2017] [Accepted: 06/07/2017] [Indexed: 01/18/2023]
Abstract
Bile acids are synthesized from cholesterol in the liver and released into the intestine to aid the digestion of dietary lipids. The host enzymes that contribute to bile acid synthesis in the liver and the regulatory pathways that influence the composition of the total bile acid pool in the host have been well established. In addition, the gut microbiota provides unique contributions to the diversity of bile acids in the bile acid pool. Gut microbial enzymes contribute significantly to bile acid metabolism through deconjugation and dehydroxylation reactions to generate unconjugated bile acids and secondary bile acids. These microbial enzymes (which include bile salt hydrolase (BSH) and bile acid-inducible (BAI) enzymes) are essential for bile acid homeostasis in the host and represent a vital contribution of the gut microbiome to host health. Perturbation of the gut microbiota in disease states may therefore significantly influence bile acid signatures in the host, especially in the context of gastrointestinal or systemic disease. Given that bile acids are ligands for host cell receptors (including the FXR, TGR5 and Vitamin D Receptor) alterations to microbial enzymes and associated changes to bile acid signatures have significant consequences for the host. In this review we examine the contribution of microbial enzymes to the process of bile acid metabolism in the host and discuss the implications for microbe-host signalling in the context of C. difficile infection, inflammatory bowel disease and other disease states.
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Affiliation(s)
- Sarah L Long
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; School of Pharmacy, University College Cork, Cork, Ireland.
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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30
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Song C, Wang B, Tan J, Zhu L, Lou D. Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics. Sci Rep 2017; 7:45495. [PMID: 28436439 PMCID: PMC5402301 DOI: 10.1038/srep45495] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/28/2017] [Indexed: 12/16/2022] Open
Abstract
Tauroursodeoxycholic acid (TUDCA) has been used to treat many diseases effectively. 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 7β-hydroxysteroid dehydrogenase (7β-HSDH) are two key enzymes that drive the efficient biosynthesis of TUDCA from taurochenodeoxycholic acid (TCDCA) in vitro. In this study, a metagenomic approach was used to isolate 7α- and 7β-HSDHs from fecal samples of black bears. Five new 7α-HSDHs and one new 7β-HSDH enzyme were discovered and identified from the gut microbiota of black bears, and four of them presented good enzymatic properties. Our data also suggest cooperation in the biotransformation of TUDCA by the gut microbiota in black bears. In conclusion, this work expands the natural enzyme bank of HSDHs, provides promising candidate enzymes for application in the biosynthesis TUDCA and the epimerization reaction of bile acids at the C-7 position, and provides a data set for the discovery of novel enzymes in the gut micriobiome of black bears.
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Affiliation(s)
- Can Song
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological & Chemical engineering, Chongqing University of Education, Chongqing 400067, China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Deshuai Lou
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
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31
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Bakonyi D, Hummel W. Cloning, expression, and biochemical characterization of a novel NADP +-dependent 7α-hydroxysteroid dehydrogenase from Clostridium difficile and its application for the oxidation of bile acids. Enzyme Microb Technol 2016; 99:16-24. [PMID: 28193327 DOI: 10.1016/j.enzmictec.2016.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/24/2016] [Accepted: 12/26/2016] [Indexed: 01/25/2023]
Abstract
A gene encoding a novel 7α-specific NADP+-dependent hydroxysteroid dehydrogenase from Clostridium difficile was cloned and heterologously expressed in Escherichia coli. The enzyme was purified using an N-terminal hexa-his-tag and biochemically characterized. The optimum temperature is at 60°C, but the enzyme is inactivated at this temperature with a half-life time of 5min. Contrary to other known 7α-HSDHs, for example from Clostridium sardiniense or E. coli, the enzyme from C. difficile does not display a substrate inhibition. In order to demonstrate the applicability of this enzyme, a small-scale biotransformation of the bile acid chenodeoxycholic acid (CDCA) into 7-ketolithocholic acid (7-KLCA) was carried out with simultaneous regeneration of NADP+ using an NADPH oxidase that resulted in a complete conversion (<99%). Furthermore, by a structure-based site-directed mutagenesis, cofactor specificity of the 7α-HSDH from Clostridium difficile was altered to accept NAD(H). This mutant was biochemically characterized and compared to the wild-type.
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Affiliation(s)
- Daniel Bakonyi
- Institute of Molecular Enzyme Technology, Heinrich Heine University of Düsseldorf, Research Centre Jülich, Wilhelm-Johnen-Straße, 52426 Jülich, Germany
| | - Werner Hummel
- Institute of Molecular Enzyme Technology, Heinrich Heine University of Düsseldorf, Research Centre Jülich, Wilhelm-Johnen-Straße, 52426 Jülich, Germany.
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The three-dimensional structure of Clostridium absonum 7α-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP(H) recognition. Sci Rep 2016; 6:22885. [PMID: 26961171 PMCID: PMC4785404 DOI: 10.1038/srep22885] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/23/2016] [Indexed: 11/09/2022] Open
Abstract
7α-hydroxysteroid dehydrogenase (7α-HSDH) can catalyse the oxidation of C7 α-OH of the steroid nucleus in the bile acid metabolism. In the paper we determined the crystal structure of 7α-HSDH from Clostridium absonum (CA 7α-HSDH) complexed with taurochenodeoxycholic acid (TCDCA) and NADP(+) by X-ray diffraction, which, as a tetramer, possesses the typical α/β folding pattern. The four subunits of an asymmetric unit lie in the fact that there are the stable hydrophobic interactions between Q-axis-related subunits. Significantly, we captured an active state of the NADP(+), confirming that nicotinamide moiety of NADP(+) act as electron carrier in the dehydrogenation. On the basis of crystal structure analysis, site-directed mutagenesis and MD simulation, furthermore, we find that the guanidinium of Arg38 can form the stable cation-π interaction with the adenine ring of NADP(+), and the cation-π interaction and hydrogen bonds between Arg38 and NADP(+) have a significant anchor effect on the cofactor binding to CA 7α-HSDH.
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Devlin AS, Fischbach MA. A biosynthetic pathway for a prominent class of microbiota-derived bile acids. Nat Chem Biol 2015; 11:685-90. [PMID: 26192599 PMCID: PMC4543561 DOI: 10.1038/nchembio.1864] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/27/2015] [Indexed: 12/26/2022]
Abstract
The gut bile acid pool is millimolar in concentration, varies widely in composition among individuals, and is linked to metabolic disease and cancer. Although these molecules derive almost exclusively from the microbiota, remarkably little is known about which bacterial species and genes are responsible for their biosynthesis. Here, we report a biosynthetic pathway for the second most abundant class in the gut, iso (3β-hydroxy) bile acids, whose levels exceed 300 µM in some humans and are absent in others. We show, for the first time, that iso bile acids are produced by Ruminococcus gnavus, a far more abundant commensal than previously known producers; and that the iso bile acid pathway detoxifies deoxycholic acid, favoring the growth of the keystone genus Bacteroides. By revealing the biosynthetic genes for an abundant class of bile acids, our work sets the stage for predicting and rationally altering the composition of the bile acid pool.
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Affiliation(s)
- A Sloan Devlin
- 1] Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA. [2] California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael A Fischbach
- 1] Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA. [2] California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
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Zheng MM, Wang RF, Li CX, Xu JH. Two-step enzymatic synthesis of ursodeoxycholic acid with a new 7β-hydroxysteroid dehydrogenase from Ruminococcus torques. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.12.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Eggert T, Bakonyi D, Hummel W. Enzymatic routes for the synthesis of ursodeoxycholic acid. J Biotechnol 2014; 191:11-21. [PMID: 25131646 DOI: 10.1016/j.jbiotec.2014.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/26/2014] [Accepted: 08/06/2014] [Indexed: 02/02/2023]
Abstract
Ursodeoxycholic acid, a secondary bile acid, is used as a drug for the treatment of various liver diseases, the optimal dose comprises the range of 8-10mg/kg/day. For industrial syntheses, the structural complexity of this bile acid requires the use of an appropriate starting material as well as the application of regio- and enantio-selective enzymes for its derivatization. Most strategies for the synthesis start from cholic acid or chenodeoxycholic acid. The latter requires the conversion of the hydroxyl group at C-7 from α- into β-position in order to obtain ursodeoxycholic acid. Cholic acid on the other hand does not only require the same epimerization reaction at C-7 but the removal of the hydroxyl group at C-12 as well. There are several bacterial regio- and enantio-selective hydroxysteroid dehydrogenases (HSDHs) to carry out the desired reactions, for example 7α-HSDHs from strains of Clostridium, Bacteroides or Xanthomonas, 7β-HSDHs from Clostridium, Collinsella, or Ruminococcus, or 12α-HSDH from Clostridium or from Eggerthella. However, all these bioconversion reactions need additional steps for the regeneration of the coenzymes. Selected multi-step reaction systems for the synthesis of ursodeoxycholic acid are presented in this review.
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Affiliation(s)
- Thorsten Eggert
- evocatal GmbH, Alfred-Nobel-Str. 10, 40789 Monheim am Rhein, Germany.
| | - Daniel Bakonyi
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University of Düsseldorf, Research Centre Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Werner Hummel
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University of Düsseldorf, Research Centre Jülich, Stetternicher Forst, 52426 Jülich, Germany.
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Cai JS, Chen JH. The mechanism of enterohepatic circulation in the formation of gallstone disease. J Membr Biol 2014; 247:1067-82. [PMID: 25107305 PMCID: PMC4207937 DOI: 10.1007/s00232-014-9715-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 07/25/2014] [Indexed: 12/25/2022]
Abstract
Bile acids entering into enterohepatic circulating are primary acids synthesized from cholesterol in hepatocyte. They are secreted actively across canalicular membrane and carried in bile to gallbladder, where they are concentrated during digestion. About 95 % BAs are actively taken up from the lumen of terminal ileum efficiently, leaving only approximately 5 % (or approximately 0.5 g/d) in colon, and a fraction of bile acids are passively reabsorbed after a series of modifications in the human large intestine including deconjugation and oxidation of hydroxy groups. Bile salts hydrolysis and hydroxy group dehydrogenation reactions are performed by a broad spectrum of intestinal anaerobic bacteria. Next, hepatocyte reabsorbs bile acids from sinusoidal blood, which are carried to liver through portal vein via a series of transporters. Bile acids (BAs) transporters are critical for maintenance of the enterohepatic BAs circulation, where BAs exert their multiple physiological functions including stimulation of bile flow, intestinal absorption of lipophilic nutrients, solubilization, and excretion of cholesterol. Tight regulation of BA transporters via nuclear receptors (NRs) is necessary to maintain proper BA homeostasis. In conclusion, disturbances of enterohepatic circulation may account for pathogenesis of gallstones diseases, including BAs transporters and their regulatory NRs and the metabolism of intestinal bacterias, etc.
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Affiliation(s)
- Jian-Shan Cai
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Shanghai, 200040, People's Republic of China,
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Ji W, Chen Y, Zhang H, Zhang X, Li Z, Yu Y. Cloning, expression and characterization of a putative 7alpha-hydroxysteroid dehydrogenase in Comamonas testosteroni. Microbiol Res 2013; 169:148-54. [PMID: 23972763 DOI: 10.1016/j.micres.2013.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/18/2013] [Accepted: 07/18/2013] [Indexed: 11/28/2022]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily is a large and diverse group of genes with members found in all forms of life. Comamonas testosteroni (C. testosterone) ATCC11996 is a Gram-negative bacterium which can use steroids as carbon and energy source. In the present investigation, we found a novel SDR gene 7alpha-hydroxysteroid dehydrogenase (7α-HSD) which is located 11.9 kb upstream from hsdA with the same transcription orientation in the C. testosteroni genome. The open reading frame of this putative 7alpha-hydroxysteroid dehydrogenase gene consists of 771 bp and translates into a protein of 256 amino acids. Two consensus sequences of the SDR superfamily were found, an N-terminal Gly-X-X-X-Gly-X-Gly cofactor-binding motif and a Tyr-X-X-X-Lys segment (residues 161-165 in the 7α-HSD sequence) essential for catalytic activity of SDR proteins. To produce purified 7α-HSD protein, the 7α-HSD gene was cloned into plasmid p(ET-15b) and the over expressed protein was purified by His-tag sequence on metal chelate chromatography. To prove that 7α-HSD is involved in the metabolic pathway of steroid compounds, we constructed a 7α-HSD knock-out mutant of C. testosteroni. Compared to the wild type C. testosteroni, degradation of testosterone, estradiol and cholesterol were decreased in the 7α-HSD knock-out mutant. Furthermore, growth in the medium with testosterone, estradiol and cholesterol was impaired in 7α-HSD knock-out mutant. The results showed that 7α-HSD is involved in steroid degradation.
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Affiliation(s)
- Wei Ji
- Jilin University, College of Animal Science and Veterinary Medicine, Changchun, PR China; Changchun University of Science and Technology, School of Life Science and Technology, Changchun, PR China
| | - Yuanan Chen
- Changchun University of Science and Technology, School of Life Science and Technology, Changchun, PR China
| | - Hao Zhang
- Changchun University of Science and Technology, School of Life Science and Technology, Changchun, PR China
| | - Xiao Zhang
- Changchun University of Science and Technology, School of Life Science and Technology, Changchun, PR China
| | - Ziyi Li
- Jilin University, College of Animal Science and Veterinary Medicine, Changchun, PR China.
| | - Yuanhua Yu
- Changchun University of Science and Technology, School of Life Science and Technology, Changchun, PR China.
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Ferrandi EE, Monti D, Patel I, Kittl R, Haltrich D, Riva S, Ludwig R. Exploitation of a Laccase/Meldola’s Blue System for NAD+Regeneration in Preparative Scale Hydroxysteroid Dehydrogenase-Catalyzed Oxidations. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200429] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gong W, Xiong G, Maser E. Cloning, expression and characterization of a novel short-chain dehydrogenase/reductase (SDRx) in Comamonas testosteroni. J Steroid Biochem Mol Biol 2012; 129:15-21. [PMID: 21111045 DOI: 10.1016/j.jsbmb.2010.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 11/16/2010] [Indexed: 11/25/2022]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily is a large and diverse group of genes with members found in all forms of life. Comamonas testosteroni ATCC11996 is a Gram-negative bacterium which can use steroids as carbon and energy source. In previous investigations, we have identified 3α-hydroxysteroid dehydrogenase/carbonyl reductase (3α-HSD/CR) from C. testosteroni as a member of the SDR superfamily that catalyzes the reversible interconversion of hydroxyl and oxo groups at position 3 of the steroid nucleus of a great variety of C(19-27) steroids. In addition, 3α-HSD/CR was shown to mediate the carbonyl reduction of non-steroidal aldehydes and ketones. Interestingly, the 3α-HSD/CR gene (hsdA) expression is induced by steroids such as testosterone and progesterone. In the present investigation, we found a novel SDR gene (SDRx) which is located 3.6kb downstream from hsdA with the same transcription orientation in the C. testosteroni genome. The open reading frame of this SDRx consists of 768bp and translates into a protein of 255 amino acids. Two consensus sequences of the SDR superfamily were found, an N-terminal Gly-X-X-X-Gly-X-Gly cofactor-binding motif and a Tyr-X-X-X-Lys segment (residues 160-164 in the SDRx sequence) essential for catalytic activity of SDR proteins. Phylogenetic analyses indicated that the novel SDRx gene codes for 7α-hydroxysteroid dehydrogenase (7α-HSD) in C. testosteroni which is active in steroid metabolism. To produce purified SDRx protein, the SDRx gene was cloned into plasmid pET-15b and the overexpressed protein was purified by its His-tag sequence on metal chelate chromatography. To prove that SDRx is involved in the metabolic pathway of steroid compounds, we constructed an SDRx knock-out mutant of C. testosteroni. Compared to wild type C. testosteroni, degradation of the steroids testosterone and estradiol decreased in the SDRx knock-out mutant. Furthermore, growth on the steroids cholic acid, estradiol and testosterone was impaired in the SDRx knock-out strain. Combined, the novel SDRx in C. testosteroni was identified as 7α-HSD that is involved in steroid degradation. Article from a special issue on steroids and microorganisms.
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Affiliation(s)
- Wenjie Gong
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School, Schleswig-Holstein, Campus Kiel, Kiel, Germany
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40
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Kisiela M, Skarka A, Ebert B, Maser E. Hydroxysteroid dehydrogenases (HSDs) in bacteria: a bioinformatic perspective. J Steroid Biochem Mol Biol 2012; 129:31-46. [PMID: 21884790 DOI: 10.1016/j.jsbmb.2011.08.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 08/01/2011] [Accepted: 08/07/2011] [Indexed: 12/15/2022]
Abstract
Steroidal compounds including cholesterol, bile acids and steroid hormones play a central role in various physiological processes such as cell signaling, growth, reproduction, and energy homeostasis. Hydroxysteroid dehydrogenases (HSDs), which belong to the superfamily of short-chain dehydrogenases/reductases (SDR) or aldo-keto reductases (AKR), are important enzymes involved in the steroid hormone metabolism. HSDs function as an enzymatic switch that controls the access of receptor-active steroids to nuclear hormone receptors and thereby mediate a fine-tuning of the steroid response. The aim of this study was the identification of classified functional HSDs and the bioinformatic annotation of these proteins in all complete sequenced bacterial genomes followed by a phylogenetic analysis. For the bioinformatic annotation we constructed specific hidden Markov models in an iterative approach to provide a reliable identification for the specific catalytic groups of HSDs. Here, we show a detailed phylogenetic analysis of 3α-, 7α-, 12α-HSDs and two further functional related enzymes (3-ketosteroid-Δ(1)-dehydrogenase, 3-ketosteroid-Δ(4)(5α)-dehydrogenase) from the superfamily of SDRs. For some bacteria that have been previously reported to posses a specific HSD activity, we could annotate the corresponding HSD protein. The dominating phyla that were identified to express HSDs were that of Actinobacteria, Proteobacteria, and Firmicutes. Moreover, some evolutionarily more ancient microorganisms (e.g., Cyanobacteria and Euryachaeota) were found as well. A large number of HSD-expressing bacteria constitute the normal human gastro-intestinal flora. Another group of bacteria were originally isolated from natural habitats like seawater, soil, marine and permafrost sediments. These bacteria include polycyclic aromatic hydrocarbons-degrading species such as Pseudomonas, Burkholderia and Rhodococcus. In conclusion, HSDs are found in a wide variety of microorganisms including bacteria and archaea, suggesting that steroid metabolism is an evolutionarily conserved mechanism that might serve different functions such as nutrient supply and signaling. Article from a special issue on steroids and microorganisms.
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Affiliation(s)
- Michael Kisiela
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
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41
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In search of sustainable chemical processes: cloning, recombinant expression, and functional characterization of the 7α- and 7β-hydroxysteroid dehydrogenases from Clostridium absonum. Appl Microbiol Biotechnol 2011; 95:1221-33. [PMID: 22198717 DOI: 10.1007/s00253-011-3798-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 10/14/2022]
Abstract
Nicotinamide adenine dinucleotide phosphate-dependent 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 7β-hydroxysteroid dehydrogenases (7β-HSDH) from Clostridium absonum catalyze the epimerization of primary bile acids through 7-keto bile acid intermediates and may be suitable as biocatalysts for the synthesis of bile acids derivatives of pharmacological interest. C. absonum 7α-HSDH has been purified to homogeneity and the N-terminal sequence has been determined by Edman sequencing. After PCR amplifications of a gene fragment with degenerate primers, cloning of the complete gene (786 nt) has been achieved by sequencing of C. absonum genomic DNA. The sequence coding for the 7β-HSDH (783 nt) has been obtained by sequencing of the genomic DNA region flanking the 5' termini of 7α-HSDH gene, the two genes being contiguous and presumably part of the same operon. After insertion in suitable expression vectors, both HSDHs have been successfully produced in recombinant form in Escherichia coli, purified by affinity chromatography and submitted to kinetic analysis for determination of Michaelis constants (K (m)) and specificity constants (k (cat)/K (m)) in the presence of various bile acids derivatives. Both enzymes showed a very strong substrate inhibition with all the tested substrates. The lowest K (S) values were observed with chenodeoxycholic acid and 12-ketochenodeoxycholic acid as substrates in the case of 7α-HSDH, whereas ursocholic acid was the most effective inhibitor of 7β-HSDH activity.
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42
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Liu Y, Lv T, Ren J, Wang M, Wu Q, Zhu D. The catalytic promiscuity of a microbial 7α-hydroxysteroid dehydrogenase. Reduction of non-steroidal carbonyl compounds. Steroids 2011; 76:1136-40. [PMID: 21600233 DOI: 10.1016/j.steroids.2011.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 04/13/2011] [Accepted: 05/01/2011] [Indexed: 10/18/2022]
Abstract
A thermostable 7α-hydroxysteroid dehydrogenase from Bacteroides fragilis ATCC 25285 was found to catalyze the reduction of various benzaldehyde analogues to their corresponding benzyl alcohols. The enzyme activity was dependent upon the substituent on the benzene ring of the substrates. Benzaldehydes with electron-withdrawing substituent usually showed higher activity than those with electron-donating groups. Furthermore, this enzyme was tolerant to some organic solvents. These results together with previous studies suggested that 7α-hydroxysteroid dehydrogenase from B. fragilis might play multiple functional roles in biosynthesis and metabolism of bile acids, and in the detoxification of xenobiotics containing carbonyl groups in the large intestine. In addition, its broad substrate spectrum offers great potential for finding applications not only in the synthesis of steroidal compounds of pharmaceutical importance, but also for the production of other high-value fine chemicals.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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43
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Monti D, Ferrandi EE, Zanellato I, Hua L, Polentini F, Carrea G, Riva S. One-Pot Multienzymatic Synthesis of 12-Ketoursodeoxycholic Acid: Subtle Cofactor Specificities Rule the Reaction Equilibria of Five Biocatalysts Working in a Row. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200800727] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Lepercq P, Hermier D, David O, Michelin R, Gibard C, Beguet F, Relano P, Cayuela C, Juste C. Increasing ursodeoxycholic acid in the enterohepatic circulation of pigs through the administration of living bacteria. Br J Nutr 2007; 93:457-69. [PMID: 15946407 DOI: 10.1079/bjn20041386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We investigated the feasibility of increasing ursodeoxycholic acid (UDCA) in the enterohepatic circulation of pigs by administering living bacteria capable of epimerising endogenous amidated chenodeoxycholic acid (CDCA) to UDCA. We first demonstrated that combining Bifidobacterium animalis DN-173 010, as a bile salt-hydrolysing bacterium, and Clostridium absonum ATCC 27555, as a CDCA to UDCA epimerising bacterium, led to the efficient epimerisation of glyco- and tauro-CDCA in vitro, with respective UDCA yields of 55·8 (se 2·8) and 36·6 (se 1·5)%. This strain combination was then administered to hypercholesterolaemic pigs over a 3-week period, as two daily preprandial doses of either viable (six experimental pigs) or heat-inactivated bacteria (six controls). The main effects of treatment were on unconjugated bile acids (P=0·035) and UDCA (P<0·0001) absorbed into the portal vein, which increased 1·6–1·7- and 3·5–7·5-fold, respectively, under administration of living compared with inactivated bacteria. In bile, UDCA did not increase significantly, but the increase in biliary lithocholic acid with time in the controls was not observed in the experimental pigs (P=0·007), and the same trend was observed in faeces. All other variables (biliary lipid equilibrium, plasma lipid levels and partition of cholesterol between the different lipoprotein classes) remained unaffected by treatment throughout the duration of the experiment. In conclusion, it is feasible to increase the bioavailability of UDCA to the intestine and the liver by administering active bacteria. This may represent an interesting new probiotic activity, provided that in future it could be expressed by a safe food micro-organism.
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Affiliation(s)
- Pascale Lepercq
- Unité d'Ecologie et de Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, France
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45
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Zhu D, Yang Y, Buynak JD, Hua L. Stereoselective ketone reduction by a carbonyl reductase from Sporobolomyces salmonicolor. Substrate specificity, enantioselectivity and enzyme-substrate docking studies. Org Biomol Chem 2006; 4:2690-5. [PMID: 16826293 DOI: 10.1039/b606001c] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In our effort to search for effective carbonyl reductases, the activity and enantioselectivity of a carbonyl reductase from Sporobolomyces salmonicolor have been evaluated toward the reduction of a variety of ketones. This carbonyl reductase (SSCR) reduces a broad spectrum of ketones including aliphatic and aromatic ketones, as well as alpha- and beta-ketoesters. Among these substrates, SSCR shows highest activity for the reduction of alpha-ketoesters. Aromatic alpha-ketoesters are reduced to (S)-alpha-hydroxy esters, while (R)-enantiomers are obtained from the reduction of aliphatic counterparts. This interesting observation is consistent with enzyme-substrate docking studies, which show that hydride transfer occurs at the different faces of carbonyl group for aromatic and aliphatic alpha-ketoesters. It is worthy to note that sterically bulky ketone substrates, such as 2'-methoxyacetophenone, 1-adamantyl methyl ketone, ethyl 4,4-dimethyl-3-oxopentanoate and ethyl 3,3-dimethyl-2-oxobutanoate, are reduced to the corresponding alcohols with excellent optical purity. Thus, SSCR possesses an unusually broad substrate specificity and is especially useful for the reduction of ketones with sterically bulky substituents.
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Affiliation(s)
- Dunming Zhu
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, USA
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46
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Zhu D, Stearns JE, Ramirez M, Hua L. Enzymatic enantioselective reduction of α-ketoesters by a thermostable 7α-hydroxysteroid dehydrogenase from Bacteroides fragilis. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.02.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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Abstract
Secondary bile acids, produced solely by intestinal bacteria, can accumulate to high levels in the enterohepatic circulation of some individuals and may contribute to the pathogenesis of colon cancer, gallstones, and other gastrointestinal (GI) diseases. Bile salt hydrolysis and hydroxy group dehydrogenation reactions are carried out by a broad spectrum of intestinal anaerobic bacteria, whereas bile acid 7-dehydroxylation appears restricted to a limited number of intestinal anaerobes representing a small fraction of the total colonic flora. Microbial enzymes modifying bile salts differ between species with respect to pH optima, enzyme kinetics, substrate specificity, cellular location, and possibly physiological function. Crystallization, site-directed mutagenesis, and comparisons of protein secondary structure have provided insight into the mechanisms of several bile acid-biotransforming enzymatic reactions. Molecular cloning of genes encoding bile salt-modifying enzymes has facilitated the understanding of the genetic organization of these pathways and is a means of developing probes for the detection of bile salt-modifying bacteria. The potential exists for altering the bile acid pool by targeting key enzymes in the 7alpha/beta-dehydroxylation pathway through the development of pharmaceuticals or sequestering bile acids biologically in probiotic bacteria, which may result in their effective removal from the host after excretion.
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Affiliation(s)
- Jason M Ridlon
- Department of Microbiology/Immunology, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA
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49
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Lepercq P, Gérard P, Béguet F, Raibaud P, Grill JP, Relano P, Cayuela C, Juste C. Epimerization of chenodeoxycholic acid to ursodeoxycholic acid byClostridium baratiiisolated from human feces. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09568.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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