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Deng WH, Liao RZ. Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. J Chem Inf Model 2024; 64:4168-4179. [PMID: 38745447 DOI: 10.1021/acs.jcim.4c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydroxyprolines are abundant in nature and widely utilized by many living organisms. Isomerization of trans-4-hydroxy-d-proline (t4D-HP) to generate 2-amino-4-ketopentanoate has been found to need a glycyl radical enzyme HplG, which catalyzes the cleavage of the C-N bond, while dehydration of trans-4-hydroxy-l-proline involves a homologous enzyme of HplG. Herein, molecular dynamics simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to understand the reaction mechanism of HplG. Two possible reaction pathways of HplG have been explored to decipher the origin of its chemoselectivity. The QM/MM calculations reveal that the isomerization proceeds via an initial hydrogen shift from the Cγ site of t4D-HP to a catalytic cysteine radical, followed by cleavage of the Cδ-N bond in t4D-HP to form a radical intermediate that captures a hydrogen atom from the cysteine. Activation of the Cδ-H bond in t4D-HP to bring about dehydration of t4D-HP possesses an extremely high energy barrier, thus rendering the dehydration pathway implausible in HplG. On the basis of the current calculations, conserved residue Glu429 plays a pivotal role in the isomerization pathway: the hydrogen bonding between it and t4D-HP weakens the hydroxyalkyl Cγ-Hγ bond, and it acts as a proton acceptor to trigger the cleavage of the C-N bond in t4D-HP. Our current QM/MM calculations rationalize the origin of the experimentally observed chemoselectivity of HplG and propose an H-bond-assisted bond activation strategy in radical-containing enzymes. These findings have general implications on radical-mediated enzymatic catalysis and expand our understanding of how nature wisely and selectively activates the C-H bond to modulate catalytic selectivity.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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2
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Jiang L, Song C, Ai C, Wen C, Song S. Modulation effect of sulfated polysaccharide from Sargassum fusiforme on gut microbiota and their metabolites in vitro fermentation. Front Nutr 2024; 11:1400063. [PMID: 38751743 PMCID: PMC11094809 DOI: 10.3389/fnut.2024.1400063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
The present study demonstrated the digestion behavior and fermentation characteristics of a sulfated polysaccharide from Sargassum fusiforme (SFSP) in the simulated digestion tract environment. The results showed that the molecular weight of two components in SFSP could not be changed by simulated digestion, and no free monosaccharide was produced. This indicates that most of SFSP can reach the colon as prototypes. During the fermentation with human intestinal flora in vitro, the higher-molecular-weight component of SFSP was utilized, the total sugar content decreased by 16%, the reducing sugar content increased, and the galactose content in monosaccharide composition decreased relatively. This indicates that SFSP can be selectively utilized by human intestinal flora. At the same time, SFSP also changed the structure of intestinal flora. Compared with the blank group, SFSP significantly increased the abundance of Bacteroidetes and decreased the abundance of Firmicutes. At the genus level, the abundances of Bacteroides and Megamonas increased, while the abundances of Shigella, Klebsiella, and Collinsella decreased. Moreover, the concentrations of total short-chain fatty acids (SCFAs), acetic, propionic and n-butyric acids significantly increased compared to the blank group. SFSP could down-regulate the contents of trimethylamine, piperidone and secondary bile acid in fermentation broth. The contents of nicotinic acid, pantothenic acid and other organic acids were increased. Therefore, SFSP shows significant potential to regulate gut microbiota and promote human health.
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Affiliation(s)
| | | | | | | | - Shuang Song
- SKL of Marine Food Processing and Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Liaoning Key Laboratory of Food Nutrition and Health, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
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3
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Feng X, Deng M, Zhang L, Pan Q. Impact of gut microbiota and associated mechanisms on postprandial glucose levels in patients with diabetes. J Transl Int Med 2023; 11:363-371. [PMID: 38130636 PMCID: PMC10732577 DOI: 10.2478/jtim-2023-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Diabetes and its complications are serious medical and global burdens, often manifesting as postprandial hyperglycemia. In recent years, considerable research attention has focused on relationships between the gut microbiota and circulating postprandial glucose (PPG). Different population studies have suggested that PPG is closely related to the gut microbiota which may impact PPG via short-chain fatty acids (SCFAs), bile acids (BAs) and trimethylamine N-oxide (TMAO). Studies now show that gut microbiota models can predict PPG, with individualized nutrition intervention strategies used to regulate gut microbiota and improve glucose metabolism to facilitate the precision treatment of diabetes. However, few studies have been conducted in patients with diabetes. Therefore, little is known about the relationships between the gut microbiota and PPG in this cohort. Thus, more research is required to identify key gut microbiota and associated metabolites and pathways impacting PPG to provide potential therapeutic targets for PPG.
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Affiliation(s)
- Xinyuan Feng
- Department of Endocrinology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Beijing100730 ,China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing100730, China
| | - Mingqun Deng
- Department of Endocrinology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Beijing100730 ,China
| | - Lina Zhang
- Department of Endocrinology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Beijing100730 ,China
| | - Qi Pan
- Department of Endocrinology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Beijing100730 ,China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing100730, China
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4
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Kaufmann B, Seyfried N, Hartmann D, Hartmann P. Probiotics, prebiotics, and synbiotics in nonalcoholic fatty liver disease and alcohol-associated liver disease. Am J Physiol Gastrointest Liver Physiol 2023; 325:G42-G61. [PMID: 37129252 PMCID: PMC10312326 DOI: 10.1152/ajpgi.00017.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
The use of probiotics, prebiotics, and synbiotics has become an important therapy in numerous gastrointestinal diseases in recent years. Modifying the gut microbiota, this therapeutic approach helps to restore a healthy microbiome. Nonalcoholic fatty liver disease and alcohol-associated liver disease are among the leading causes of chronic liver disease worldwide. A disrupted intestinal barrier, microbial translocation, and an altered gut microbiome metabolism, or metabolome, are crucial in the pathogenesis of these chronic liver diseases. As pro-, pre-, and synbiotics modulate these targets, they were identified as possible new treatment options for liver disease. In this review, we highlight the current findings on clinical and mechanistic effects of this therapeutic approach in nonalcoholic fatty liver disease and alcohol-associated liver disease.
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Affiliation(s)
- Benedikt Kaufmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Nick Seyfried
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Daniel Hartmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Phillipp Hartmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States
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5
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Guiducci L, Nicolini G, Forini F. Dietary Patterns, Gut Microbiota Remodeling, and Cardiometabolic Disease. Metabolites 2023; 13:760. [PMID: 37367916 DOI: 10.3390/metabo13060760] [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: 05/24/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
The cardiovascular and metabolic disorders, collectively known as cardiometabolic disease (CMD), are high morbidity and mortality pathologies associated with lower quality of life and increasing health-care costs. The influence of the gut microbiota (GM) in dictating the interpersonal variability in CMD susceptibility, progression and treatment response is beginning to be deciphered, as is the mutualistic relation established between the GM and diet. In particular, dietary factors emerge as pivotal determinants shaping the architecture and function of resident microorganisms in the human gut. In turn, intestinal microbes influence the absorption, metabolism, and storage of ingested nutrients, with potentially profound effects on host physiology. Herein, we present an updated overview on major effects of dietary components on the GM, highlighting the beneficial and detrimental consequences of diet-microbiota crosstalk in the setting of CMD. We also discuss the promises and challenges of integrating microbiome data in dietary planning aimed at restraining CMD onset and progression with a more personalized nutritional approach.
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Affiliation(s)
- Letizia Guiducci
- CNR Institute of Clinical Physiology, Via Moruzzi 1, 56124 Pisa, Italy
| | | | - Francesca Forini
- CNR Institute of Clinical Physiology, Via Moruzzi 1, 56124 Pisa, Italy
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6
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Mutengo KH, Masenga SK, Mweemba A, Mutale W, Kirabo A. Gut microbiota dependant trimethylamine N-oxide and hypertension. Front Physiol 2023; 14:1075641. [PMID: 37089429 PMCID: PMC10118022 DOI: 10.3389/fphys.2023.1075641] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
The human gut microbiota environment is constantly changing and some specific changes influence the host's metabolic, immune, and neuroendocrine functions. Emerging evidence of the gut microbiota's role in the development of cardiovascular disease (CVD) including hypertension is remarkable. There is evidence showing that alterations in the gut microbiota and especially the gut-dependant metabolite trimethylamine N-oxide is associated with hypertension. However, there is a scarcity of literature addressing the role of trimethylamine N-oxide in hypertension pathogenesis. In this review, we discuss the impact of the gut microbiota and gut microbiota dependant trimethylamine N-oxide in the pathogenesis of hypertension. We present evidence from both human and animal studies and further discuss new insights relating to potential therapies for managing hypertension by altering the gut microbiota.
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Affiliation(s)
- Katongo H. Mutengo
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone, Zambia
- Schools of Public Health and Medicine, University of Zambia, Lusaka, Zambia
| | - Sepiso K. Masenga
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone, Zambia
- Schools of Public Health and Medicine, University of Zambia, Lusaka, Zambia
| | - Aggrey Mweemba
- Department of Medicine, Levy Mwanawasa Medical University, Lusaka, Zambia
| | - Wilbroad Mutale
- School of Public Health, University of Zambia, Lusaka, Zambia
| | - Annet Kirabo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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7
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Benson TW, Conrad KA, Li XS, Wang Z, Helsley RN, Schugar RC, Coughlin TM, Wadding-Lee C, Fleifil S, Russell HM, Stone T, Brooks M, Buffa JA, Mani K, Björck M, Wanhainen A, Sangwan N, Biddinger S, Bhandari R, Ademoya A, Pascual C, Tang WW, Tranter M, Cameron SJ, Brown JM, Hazen SL, Owens AP. Gut Microbiota-Derived Trimethylamine N-Oxide Contributes to Abdominal Aortic Aneurysm Through Inflammatory and Apoptotic Mechanisms. Circulation 2023; 147:1079-1096. [PMID: 37011073 PMCID: PMC10071415 DOI: 10.1161/circulationaha.122.060573] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 02/07/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND Large-scale human and mechanistic mouse studies indicate a strong relationship between the microbiome-dependent metabolite trimethylamine N-oxide (TMAO) and several cardiometabolic diseases. This study aims to investigate the role of TMAO in the pathogenesis of abdominal aortic aneurysm (AAA) and target its parent microbes as a potential pharmacological intervention. METHODS TMAO and choline metabolites were examined in plasma samples, with associated clinical data, from 2 independent patient cohorts (N=2129 total). Mice were fed a high-choline diet and underwent 2 murine AAA models, angiotensin II infusion in low-density lipoprotein receptor-deficient (Ldlr-/-) mice or topical porcine pancreatic elastase in C57BL/6J mice. Gut microbial production of TMAO was inhibited through broad-spectrum antibiotics, targeted inhibition of the gut microbial choline TMA lyase (CutC/D) with fluoromethylcholine, or the use of mice genetically deficient in flavin monooxygenase 3 (Fmo3-/-). Finally, RNA sequencing of in vitro human vascular smooth muscle cells and in vivo mouse aortas was used to investigate how TMAO affects AAA. RESULTS Elevated TMAO was associated with increased AAA incidence and growth in both patient cohorts studied. Dietary choline supplementation augmented plasma TMAO and aortic diameter in both mouse models of AAA, which was suppressed with poorly absorbed oral broad-spectrum antibiotics. Treatment with fluoromethylcholine ablated TMAO production, attenuated choline-augmented aneurysm initiation, and halted progression of an established aneurysm model. In addition, Fmo3-/- mice had reduced plasma TMAO and aortic diameters and were protected from AAA rupture compared with wild-type mice. RNA sequencing and functional analyses revealed choline supplementation in mice or TMAO treatment of human vascular smooth muscle cells-augmented gene pathways associated with the endoplasmic reticulum stress response, specifically the endoplasmic reticulum stress kinase PERK. CONCLUSIONS These results define a role for gut microbiota-generated TMAO in AAA formation through upregulation of endoplasmic reticulum stress-related pathways in the aortic wall. In addition, inhibition of microbiome-derived TMAO may serve as a novel therapeutic approach for AAA treatment where none currently exist.
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Affiliation(s)
- Tyler W. Benson
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Kelsey A. Conrad
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Xinmin S. Li
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Robert N. Helsley
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rebecca C. Schugar
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Taylor M. Coughlin
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Caris Wadding-Lee
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Salma Fleifil
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Hannah M. Russell
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Timothy Stone
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Biostatistics and Bioinformatics, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Michael Brooks
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Jennifer A. Buffa
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin Mani
- Section of Vascular Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Martin Björck
- Section of Vascular Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anders Wanhainen
- Section of Vascular Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sudha Biddinger
- Division of Endocrinology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rohan Bhandari
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Hearth, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Akiirayi Ademoya
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Crystal Pascual
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - W.H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Hearth, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael Tranter
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
| | - Scott J. Cameron
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Hearth, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - J. Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stanley L. Hazen
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Hearth, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - A. Phillip Owens
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Division of Cardiovascular Health & Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
- Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0542, USA
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8
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Sánchez-Tirado E, Agüí L, González-Cortés A, Campuzano S, Yáñez-Sedeño P, Pingarrón JM. Electrochemical (Bio)Sensing Devices for Human-Microbiome-Related Biomarkers. SENSORS (BASEL, SWITZERLAND) 2023; 23:837. [PMID: 36679633 PMCID: PMC9864681 DOI: 10.3390/s23020837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The study of the human microbiome is a multidisciplinary area ranging from the field of technology to that of personalized medicine. The possibility of using microbiota biomarkers to improve the diagnosis and monitoring of diseases (e.g., cancer), health conditions (e.g., obesity) or relevant processes (e.g., aging) has raised great expectations, also in the field of bioelectroanalytical chemistry. The well-known advantages of electrochemical biosensors-high sensitivity, fast response, and the possibility of miniaturization, together with the potential for new nanomaterials to improve their design and performance-position them as unique tools to provide a better understanding of the entities of the human microbiome and raise the prospect of huge and important developments in the coming years. This review article compiles recent applications of electrochemical (bio)sensors for monitoring microbial metabolites and disease biomarkers related to different types of human microbiome, with a special focus on the gastrointestinal microbiome. Examples of electrochemical devices applied to real samples are critically discussed, as well as challenges to be faced and where future developments are expected to go.
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9
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Simpson JB, Redinbo MR. Multi-omic analysis of host-microbial interactions central to the gut-brain axis. Mol Omics 2022; 18:896-907. [PMID: 36169030 DOI: 10.1039/d2mo00205a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The gut microbiota impact numerous aspects of human physiology, including the central nervous system (CNS). Emerging work is now focusing on the microbial factors underlying the bi-directional communication network linking host and microbial systems within the gastrointestinal tract to the CNS, the "gut-brain axis". Neurotransmitters are key coordinators of this network, and their dysregulation has been linked to numerous neurological disease states. As the bioavailability of neurotransmitters is modified by gut microbes, it is critical to unravel the influence of the microbiota on neurotransmitters in the context of the gut-brain axis. Here we review foundational studies that defined molecular relationships between the microbiota, neurotransmitters, and the gut-brain axis. We examine links between the gut microbiome, behavior, and neurological diseases, as well as microbial influences on neurotransmitter bioavailability and physiology. Finally, we review multi-omics technologies uniquely applicable to this area, including high-throughput genetics, modern metabolomics, structure-guided metagenomics, targeted proteomics, and chemogenetics. Interdisciplinary studies will continue to drive the discovery of molecular mechanisms linking the gut microbiota to clinical manifestations of neurobiology.
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Affiliation(s)
- Joshua B Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, USA
- Department of Biochemistry & Biophysics, Department of Microbiology & Immunology, and the Integrated Program in Biological & Genome Sciences, University of North Carolina at Chapel Hill, USA.
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10
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Zhou P, Zhao XN, Ma YY, Tang TJ, Wang SS, Wang L, Huang JL. Virtual screening analysis of natural flavonoids as trimethylamine (TMA)-lyase inhibitors for coronary heart disease. J Food Biochem 2022; 46:e14376. [PMID: 35945702 DOI: 10.1111/jfbc.14376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 01/13/2023]
Abstract
Coronary heart disease (CHD) is defined by atherosclerosis, which can result in stenosis or blockage of the arterial cavity, leading to ischemic cardiac diseases such as angina and myocardial infarction. Accumulating evidence indicates that the gut microbiota plays a vital role in the beginning and progression of CHD. The gut microbial metabolite, trimethylamine-N-oxide (TMAO), is intimately linked to the pathophysiology of CHD. TMAO is formed when trimethylamine (TMA) is converted by flavin-containing monooxygenases in the hepatocytes. Therefore, inhibition of TMA production is essential to reduce TMAO levels. Flavonoids may reduce the risk of death from cardiovascular disease. In this article, we reviewed and evaluated twenty-two flavonoids for the therapy of CHD based on their inhibition of TMA-lyase by molecular docking. Docking results revealed that baicalein, fisetin, acacetin, and myricetin in flavonoid aglycones, and baicalin, naringin, and hesperidin in flavonoid glycosides had a good binding effect with TMA-lyase. This indicates that these chemicals were the most active and could be used as lead compounds for structural modification in the future. PRACTICAL APPLICATIONS: Flavonoids are a large class of polyphenolic compounds found in fruits, vegetables, flowers, tea, and herbal medicines, which are inexorably metabolized and transformed into bioactive metabolites by α-rhamnosidase, β-glucuronidase, β-glucosidase, and nitroreductase produced by the gut microbiota, which plays a beneficial role in the prevention and treatment of cardiovascular diseases. Because flavonoids protect the cardiovascular system and regulate the gut microbiota, and the gut microbiota is directly connected to TMAO, thus, reducing TMAO levels involves blocking the transition of TMA to TMAO, which may be performed by reducing TMA synthesis. Molecular docking results found that baicalein, fisetin, acacetin, and myricetin in flavonoid aglycones, and baicalin, naringin, and hesperidin in flavonoid glycosides had good binding effects on TMA-lyase, which were the most active and could be used as lead compounds for structural modification.
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Affiliation(s)
- Peng Zhou
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, People's Republic of China
| | - Xiao-Ni Zhao
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China
| | - Yao-Yao Ma
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China
| | - Tong-Juan Tang
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China
| | - Shu-Shu Wang
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China
| | - Liang Wang
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, People's Republic of China
| | - Jin-Ling Huang
- Department of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People's Republic of China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, People's Republic of China
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11
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Li J, Huang P, Cheng W, Niu Q. Stilbene-based derivatives as potential inhibitors of trimethylamine (TMA)-lyase affect gut microbiota in coronary heart disease. Food Sci Nutr 2022; 11:93-100. [PMID: 36655110 PMCID: PMC9834892 DOI: 10.1002/fsn3.3046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 08/05/2022] [Accepted: 08/14/2022] [Indexed: 01/21/2023] Open
Abstract
Coronary heart disease (CHD) is defined by atherosclerosis, which may result in stenosis or blockage of the arterial cavity, leading to ischemic cardiac diseases such as angina and myocardial infarction (MI). Accumulating evidence indicates that the gut microbiota play a critical role in the initiation and progression of CHD. The gut microbial metabolite trimethylamine N-oxide (TMAO) is intimately linked to the pathophysiology of CHD. The hepatic flavin-containing monooxygenases (FMOs) convert trimethylamine (TMA) to TMAO. As a result, it is critical to prevent TMA generation. Stilbenes could reduce cardiovascular disease mortality. Twelve stilbenes with inhibitory activity against TMA-lyase were compiled and evaluated in this study. Docking results showed Resveratroloside had the highest Vina score, indicating that it was the most active and might be employed as a lead molecule for further structural modification.
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Affiliation(s)
- Jincai Li
- School of Traditional Chinese MedicineBozhou UniversityBozhouChina
| | - Peng Huang
- School of PharmacyAnhui University of Chinese MedicineHefeiChina
| | - Wangxing Cheng
- School of PharmacyAnhui University of Chinese MedicineHefeiChina
| | - Qian Niu
- Department of PharmacyBozhou Vocational and Technical CollegeBozhouChina
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12
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Zhou P, Kang JL, Cheng QQ, Chen MT, Xie Y, Zhou H. Therapeutic potential of traditional Chinese medicine against atherosclerosis: Targeting trimethylamine N-oxide. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 104:154305. [PMID: 35792446 DOI: 10.1016/j.phymed.2022.154305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Recent studies have shown that plasma trimethylamine-N-oxide (TMAO) level is highly correlated with the risk of atherosclerosis (AS), and the elevated level is significantly positively correlated with the incidence of AS. PURPOSE The purpose of this article is to offer a useful summary of the correlation between TMAO and AS, and the effect of herbal monomers, herbal extracts, and formulas on anti-atherosclerosis mediated by TMAO. METHOD The data contained in this article comes from PubMed, Web of Science, and China National Knowledge Infrastructure. RESULTS This review discusses the main mechanism of AS induced by TMAO, including endothelial dysfunction, macrophage foaming, platelet reactivity, and cholesterol metabolism, and summarizes 6 herb monomers, 5 herb extracts, and 2 formulas that have been tested for their anti-TMAO activity. CONCLUSION The current understanding of possible ways to reduce TMAO generation is discussed, with the effect and potential of herb monomers, herb extracts, and formulas highlighted.
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Affiliation(s)
- Peng Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Anhui, PR China; Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, PR China
| | - Jun-Li Kang
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, PR China
| | - Qi-Qing Cheng
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, PR China
| | - Ming-Tai Chen
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, PR China; Department of Cardiovascular Disease, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese medicine, Shenzhen, PR China
| | - Ying Xie
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangdong, PR China; Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, PR China
| | - Hua Zhou
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangdong, PR China; Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, PR China.
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13
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Liu Y, Zheng G, Jin X, Fan T, Chen Z, Sheng X. Influence of Gut Microbiota and Trimethylamine N-Oxide in Patients with Coronary Heart Disease. Int Heart J 2022; 63:683-691. [PMID: 35831155 DOI: 10.1536/ihj.22-070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the current study, the gut microbiota of patients with and without coronary heart disease was compared and the relationship between gut microbiota distribution, intending to reveal the role of gut microbiota in the coronary atherosclerosis process, was investigated.This study included 50 patients diagnosed with coronary heart disease (CHD) who received conventional coronary angiography or computed tomography angiography and 50 patients with CHD at Changshu No. 2 People's Hospital, Suzhou, China, from May 2020 to January 2021. Trimethylamine N-oxide (TMAO) level was tested and feces were collected, the DNA of the gut microbiota was extracted, and the distribution by 16SrRNA gene sequencing was obtained from the two groups of patients.Plasma TMAO concentrations were significantly higher in patients with CHD (P < 0.001). In the CHD group, 22 patients with multivessel disease had a higher level of TMAO compared with the 28 patients who had the single-vessel disease (P < 0.001). No difference in the gut microbiota diversity was noted between the two groups (P < 0.001). Patients with CHD had a significantly lower proportion of Bacteroidetes phyla and more proportion of Epsilonbacteraeota phyla. At the genus level, patients with CHD had an increased abundance of Enterococcus, whereas healthy controls had significantly higher levels of Streptococcus. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 analysis found that, in the KEGG ORTHOLOGY, the level of choline trimethylamine-lyase gene expression correlated with TMAO production was higher in the fecal microbiome of the CHD group (P < 0.05).Gut microbiota and its product were expected to become a diagnostic marker and a new target for preventing CHD.
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Affiliation(s)
- Yanqi Liu
- Department of Cardiology, The Second People's Hospital of Changshu
| | - Guanqun Zheng
- Department of Cardiology, The Second People's Hospital of Changshu
| | - Xiaoqi Jin
- Department of Cardiology, The Second People's Hospital of Changshu
| | - Tao Fan
- Department of Cardiology, The Second People's Hospital of Changshu
| | - Zhixian Chen
- Department of Cardiology, The Second People's Hospital of Changshu
| | - Xiaodong Sheng
- Department of Cardiology, The Second People's Hospital of Changshu
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14
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Taniya MA, Chung HJ, Al Mamun A, Alam S, Aziz MA, Emon NU, Islam MM, Hong STS, Podder BR, Ara Mimi A, Aktar Suchi S, Xiao J. Role of Gut Microbiome in Autism Spectrum Disorder and Its Therapeutic Regulation. Front Cell Infect Microbiol 2022; 12:915701. [PMID: 35937689 PMCID: PMC9355470 DOI: 10.3389/fcimb.2022.915701] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/22/2022] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurological disorder that affects normal brain development. The recent finding of the microbiota–gut–brain axis indicates the bidirectional connection between our gut and brain, demonstrating that gut microbiota can influence many neurological disorders such as autism. Most autistic patients suffer from gastrointestinal (GI) symptoms. Many studies have shown that early colonization, mode of delivery, and antibiotic usage significantly affect the gut microbiome and the onset of autism. Microbial fermentation of plant-based fiber can produce different types of short-chain fatty acid (SCFA) that may have a beneficial or detrimental effect on the gut and neurological development of autistic patients. Several comprehensive studies of the gut microbiome and microbiota–gut–brain axis help to understand the mechanism that leads to the onset of neurological disorders and find possible treatments for autism. This review integrates the findings of recent years on the gut microbiota and ASD association, mainly focusing on the characterization of specific microbiota that leads to ASD and addressing potential therapeutic interventions to restore a healthy balance of gut microbiome composition that can treat autism-associated symptoms.
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Affiliation(s)
- Masuma Afrin Taniya
- Department of Life Sciences, School of Environment and Life Science, Independent University, Dhaka, Bangladesh
| | - Hea-Jong Chung
- Gwanju Center, Korea Basic Science Institute, Gwanju, South Korea
- *Correspondence: Hea-Jong Chung, ; Jian Xiao,
| | - Abdullah Al Mamun
- Molecular Pharmacology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Safaet Alam
- Drugs and Toxins Research Division, BCSIR Laboratories, Rajshahi, Bangladesh Council of Scientific and Industrial Research, Rajshahi, Bangladesh
| | - Md. Abdul Aziz
- Department of Pharmacy, Faculty of Pharmacy and Health Sciences, State University of Bangladesh, Dhaka, Bangladesh
| | - Nazim Uddin Emon
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Chattogram, Bangladesh
| | - Md. Minarul Islam
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, South Korea
| | - Seong-T shool Hong
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, South Korea
| | - Bristy Rani Podder
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Anjuman Ara Mimi
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Suzia Aktar Suchi
- Department of Pharmacy, College of Pharmacy, Chosun University, Gwangju, South Korea
| | - Jian Xiao
- Molecular Pharmacology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Hand Surgery and Peripheral Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Hea-Jong Chung, ; Jian Xiao,
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15
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Ma SR, Tong Q, Lin Y, Pan LB, Fu J, Peng R, Zhang XF, Zhao ZX, Li Y, Yu JB, Cong L, Han P, Zhang ZW, Yu H, Wang Y, Jiang JD. Berberine treats atherosclerosis via a vitamine-like effect down-regulating Choline-TMA-TMAO production pathway in gut microbiota. Signal Transduct Target Ther 2022; 7:207. [PMID: 35794102 PMCID: PMC9259588 DOI: 10.1038/s41392-022-01027-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/29/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Trimethylamine-N-oxide (TMAO) derived from the gut microbiota is an atherogenic metabolite. This study investigates whether or not berberine (BBR) could reduce TMAO production in the gut microbiota and treat atherosclerosis. Effects of BBR on TMAO production in the gut microbiota, as well as on plaque development in atherosclerosis were investigated in the culture of animal intestinal bacterial, HFD-fed animals and atherosclerotic patients, respectively. We found that oral BBR in animals lowers TMAO biosynthesis in intestine through interacting with the enzyme/co-enzyme of choline-trimethylamine lyase (CutC) and flavin-containing monooxygenase (FMO) in the gut microbiota. This action was performed by BBR’s metabolite dihydroberberine (a reductive BBR by nitroreductase in the gut microbiota), via a vitamine-like effect down-regulating Choline-TMA-TMAO production pathway. Oral BBR decreased TMAO production in animal intestine, lowered blood TMAO and interrupted plaque formation in blood vessels in the HFD-fed hamsters. Moreover, 21 patients with atherosclerosis exhibited the average decrease of plaque score by 3.2% after oral BBR (0.5 g, bid) for 4 months (*P < 0.05, n = 21); whereas the plaque score in patients treated with rosuvastatin plus aspirin, or clopidogrel sulfate or ticagrelor (4 months, n = 12) increased by 1.9%. TMA and TMAO in patients decreased by 38 and 29% in faeces (*P < 0.05; *P < 0.05), and 37 and 35% in plasma (***P < 0.001; *P < 0.05), after 4 months on BBR. BBR might treat atherosclerotic plaque at least partially through decreasing TMAO in a mode of action similar to that of vitamins.
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Affiliation(s)
- Shu-Rong Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Qian Tong
- The First Hospital of Jilin University, Changchun, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Li-Bin Pan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Jie Fu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Ran Peng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | | | - Zhen-Xiong Zhao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Yang Li
- The First Hospital of Jilin University, Changchun, China
| | - Jin-Bo Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Lin Cong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Pei Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Zheng-Wei Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Hang Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
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16
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Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
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Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
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17
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Duan Y, Wei Y, Xing M, Liu J, Jiang L, Lu Q, Liu X, Liu Y, Ang EL, Liao RZ, Yuchi Z, Zhao H, Zhang Y. Anaerobic Hydroxyproline Degradation Involving C-N Cleavage by a Glycyl Radical Enzyme. J Am Chem Soc 2022; 144:9715-9722. [PMID: 35611954 DOI: 10.1021/jacs.2c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxyprolines are highly abundant in nature as they are components of many structural proteins and osmolytes. Anaerobic degradation of trans-4-hydroxy-l-proline (t4L-HP) was previously found to involve the glycyl radical enzyme (GRE) t4L-HP dehydratase (HypD). Here, we report a pathway for anaerobic hydroxyproline degradation that involves a new GRE, trans-4-hydroxy-d-proline (t4D-HP) C-N-lyase (HplG). In this pathway, cis-4-hydroxy-l-proline (c4L-HP) is first isomerized to t4D-HP, followed by radical-mediated ring opening by HplG to give 2-amino-4-ketopentanoate (AKP), the first example of a ring opening reaction catalyzed by a GRE 1,2-eliminase. Subsequent cleavage by AKP thiolase (OrtAB) yields acetyl-CoA and d-alanine. We report a crystal structure of HplG in complex with t4D-HP at a resolution of 2.7 Å, providing insights into its catalytic mechanism. Different from HypD commonly identified in proline-reducing Clostridia, HplG is present in other types of fermenting bacteria, including propionate-producing bacteria, underscoring the diversity of enzymatic radical chemistry in the anaerobic microbiome.
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Affiliation(s)
- Yongxu Duan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Meining Xing
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xumei Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yanhong Liu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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18
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Hua F, Zhou P, Bao G, Ling T. Flavonoids in Lu’an GuaPian tea as potential inhibitors of TMA‐lyase in acute myocardial infarction. J Food Biochem 2022; 46:e14110. [DOI: 10.1111/jfbc.14110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Fang Hua
- School of Pharmacy Anhui Xinhua University Hefei China
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei China
| | - Peng Zhou
- Department of Integrated Traditional Chinese and Western Medicine Anhui University of Chinese Medicine Hefei China
| | - Guan‐hu Bao
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei China
| | - Tie‐jun Ling
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei China
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19
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Mousa WK, Chehadeh F, Husband S. Recent Advances in Understanding the Structure and Function of the Human Microbiome. Front Microbiol 2022; 13:825338. [PMID: 35185849 PMCID: PMC8851206 DOI: 10.3389/fmicb.2022.825338] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
Trillions of microbes live within our bodies in a deep symbiotic relationship. Microbial populations vary across body sites, driven by differences in the environment, immunological factors, and interactions between microbial species. Major advances in genome sequencing enable a better understanding of microbiome composition. However, most of the microbial taxa and species of the human microbiome are still unknown. Without revealing the identity of these microbes as a first step, we cannot appreciate their role in human health and diseases. A shift in the microbial balance, termed dysbiosis, is linked to a broad range of diseases from simple colitis and indigestion to cancer and dementia. The last decade has witnessed an explosion in microbiome research that led to a better understanding of the microbiome structure and function. This understanding leads to potential opportunities to develop next-generation microbiome-based drugs and diagnostic biomarkers. However, our understanding is limited given the highly personalized nature of the microbiome and its complex and multidirectional interactions with the host. In this review, we discuss: (1) our current knowledge of microbiome structure and factors that shape the microbial composition, (2) recent associations between microbiome dysbiosis and diseases, and (3) opportunities of new microbiome-based therapeutics. We analyze common themes, promises, gaps, and challenges of the microbiome research.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
- Department of Biology, Whitman College, Walla Walla, WA, United States
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Fadia Chehadeh
- Department of Biology, Whitman College, Walla Walla, WA, United States
| | - Shannon Husband
- Department of Biology, Whitman College, Walla Walla, WA, United States
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20
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Kashyap J, Ringiesn JR, Schwab N, Ferguson DJ. Isolation and characterization of a novel choline degrading Citrobacter amalonaticus strain from the human gut. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100157. [DOI: 10.1016/j.crmicr.2022.100157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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21
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Ramireddy L, Tsen HY, Chiang YC, Hung CY, Chen FC, Yen HT. The gene expression and bioinformatic analysis of choline trimethylamine-lyase (CutC) and its activating enzyme ( CutD) for gut microbes and comparison with their TMA production levels. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100043. [PMID: 34841334 PMCID: PMC8610359 DOI: 10.1016/j.crmicr.2021.100043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/04/2021] [Accepted: 06/13/2021] [Indexed: 12/14/2022] Open
Abstract
Analyzed the cutC and cutD gene expression and their TMA production levels. Bioinformatic analysis of cutC and cutD proteins showed conserved regions. Analysis of cutC protein showed conserved choline binding active site residues. TMA levels not only depend on cutC and cutD genes other factors are also involved.
Recent studies revealed that some intestinal microorganisms anaerobically convert choline to trimethylamine (TMA) by choline TMA-lyase (cutC). TMA is further oxidized to trimethylamine-N-oxide (TMAO), by the liver enzyme flavin-dependent monooxygenase 3 (FMO3). TMA in the serum is correlated with the risk of cardiovascular disease and some other diseases in human. The objective of this study is to study the expression levels of cutC and its activating enzyme (cutD) gene for these microorganisms and their association with TMA production. In this study, we collected 20 TMA producing bacteria strains representing 20 species, and designed primers to evaluate their gene expression levels by reverse transcription quantitative PCR (RT-qPCR). In addition, TMA production was analyzed by UPLC-MS/MS. Results showed that gene expression levels of most individual strains were different when compared with the gene expression level of their glyceraldehyde-3 phosphate dehydrogenase (GAPDH) gene and the TMA production level of gut bacteria may not correlate with their cutC/cutD gene expression levels. Bioinformatic analysis of the CutC protein showed conserved choline binding site residues; cutD showed conserved S-adenosylmethionine (SAM) and two CX2-CX2-CX3 motifs. The present study reports that the TMA production level may not only depend on cutC/cutD gene expression. Other factors may need to be investigated.
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Affiliation(s)
- Latha Ramireddy
- Department of Food Science and Technology, Hung Kuang University, Shalu District, Taichung, Taiwan, R.O.C
- Corresponding authors.
| | - Hau-Yang Tsen
- Department of Food Science and Technology, Hung Kuang University, Shalu District, Taichung, Taiwan, R.O.C
- Corresponding authors.
| | - Yu-Chen Chiang
- Department of Food Nutrition and Health Biotechnology, Asia University, Wufeng, Taichung, Taiwan, ROC
| | - Chen Ying Hung
- Department of Internal Medicine, Taipei Veterns General Hospital, Hsinchu Branch, Hsinchu, Taiwan
| | - Fu-Chih Chen
- Uni President Enterprises Corporation, Yongkang, Tainan, Taiwan
| | - Hsien- Tung Yen
- Department of Internal Medicine, Taipei Veterns General Hospital, Hsinchu Branch, Hsinchu, Taiwan
- Uni President Enterprises Corporation, Yongkang, Tainan, Taiwan
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22
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Study to Explore Plant-Derived Trimethylamine Lyase Enzyme Inhibitors to Address Gut Dysbiosis. Appl Biochem Biotechnol 2021; 194:99-123. [PMID: 34822060 DOI: 10.1007/s12010-021-03747-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/21/2021] [Indexed: 12/27/2022]
Abstract
Lifestyle complications are major health concerns around the globe and are recognized as a major factor for the development of various chronic diseases such as obesity, diabetes, inflammatory bowel diseases, cancer, and cardiac diseases. An unhealthy diet and poor lifestyle impose a serious threat to human health. Numerous studies have suggested the role of human microbiota in human health and diseases. Microbiota resides in the human body symbiotically and the composition of microorganisms is crucial for maintaining the healthy state of an individual. A dysbiotic gut microbiome is responsible for the release of toxic metabolites such as trimethylamine, lipopolysaccharides, bile acids, and uremic toxins and is associated with impaired organ functions. Dietary and herbal intervention of dysbiosis proposes a promising strategy to counteract gut alterations and repairing of the microbial ecosystem and health. The objective of the present comparative study was to observe the effect of therapeutic herbs in gut dysbiosis. In silico studies were performed to identify human microbiota associated with various diseases, ADME, and toxicity properties of phytoconstituents of "Tinospora cordifolia" and "Ocimum sanctum." Furthermore, co-interaction studies were performed to observe the affinity of selected phytochemicals against choline trimethylamine lyase, a critical enzyme involved in dysbiosis-induced human diseases. The antimicrobial potential of phytocompounds was done by the disc diffusion method. In conclusion, our work discusses the herbal intervention of gut dysbiosis and proposes a natural, safe, and effective herbal formulation to correct microbial dysbiosis and associated diseases.
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23
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Zheng S, Piao C, Liu Y, Liu X, Liu T, Zhang X, Ren J, Liu Y, Zhu B, Du J. Glycan Biosynthesis Ability of Gut Microbiota Increased in Primary Hypertension Patients Taking Antihypertension Medications and Potentially Promoted by Macrophage-Adenosine Monophosphate-Activated Protein Kinase. Front Microbiol 2021; 12:719599. [PMID: 34803940 PMCID: PMC8600050 DOI: 10.3389/fmicb.2021.719599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023] Open
Abstract
Increasing evidences suggest that the gut microbiota have their contributions to the hypertension, but the metagenomic characteristics and potential regulating mechanisms in primary hypertension patients taking antihypertension drugs are not clear yet. We carried out a metagenomic analysis in 30 primary hypertension patients taking antihypertension medications and eight healthy adults without any medication. We found that bacterial strains from species, such as Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, Klebsiella pneumoniae, and Streptococcus vestibularis, were highly increased in patients; and these strains were reported to generate glycan, short-chain fatty acid (SCFA) and trimethylamine (TMA) or be opportunistic pathogens. Meanwhile, Dorea longicatena, Eubacterium hallii, Clostridium leptum, Faecalibacterium prausnitzii, and some other strains were greatly decreased in the patient group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that ortholog groups and pathways related to glycan biosynthesis and multidrug resistance were significantly increased in the patient group, and some of the hub genes related to N-glycan biosynthesis were increased in the patient group, while those related to TMA precursor metabolism and amino acid metabolism both increased and decreased in the patient group. Metabolites tested by untargeted liquid chromatography–mass spectrometry (LC-MS) proved the decrease of acetic acid, choline, betaine, and several amino acids in patients’ fecal samples. Moreover, meta-analysis of recent studies found that almost all patients were taking at least one kind of drugs that were reported to regulate adenosine monophosphate-activated protein kinase (AMPK) pathway, so we further investigated if AMPK regulated the metagenomic changes by using angiotensin II-induced mouse hypertensive model on wild-type and macrophage-specific AMPK-knockout mice. We found that the changes in E. coli and Dorea and glycan biosynthesis-related orthologs and pathways were similar in our cohort and hypertensive wild-type mice but reversed after AMPK knockout. These results suggest that the gut microbiota-derived glycan, SCFA, TMA, and some other metabolites change in medication-taking primary hypertension patients and that medications might promote gut microbiota glycan biosynthesis through activating macrophage-AMPK.
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Affiliation(s)
- Shuai Zheng
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
| | - Chunmei Piao
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
| | - Yan Liu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
| | - Xuxia Liu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
| | - Tingting Liu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
| | - Xiaoping Zhang
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
| | - Jingyuan Ren
- Department of Hypertension, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yulei Liu
- Department of Clinic Laboratory, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Du
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, China
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24
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Goh YQ, Cheam G, Wang Y. Understanding Choline Bioavailability and Utilization: First Step Toward Personalizing Choline Nutrition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10774-10789. [PMID: 34392687 DOI: 10.1021/acs.jafc.1c03077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Choline is an essential macronutrient involved in neurotransmitter synthesis, cell-membrane signaling, lipid transport, and methyl-group metabolism. Nevertheless, the vast majority are not meeting the recommended intake requirement. Choline deficiency is linked to nonalcoholic fatty liver disease, skeletal muscle atrophy, and neurodegenerative diseases. The conversion of dietary choline to trimethylamine by gut microbiota is known for its association with atherosclerosis and may contribute to choline deficiency. Choline-utilizing bacteria constitutes less than 1% of the gut community and is modulated by lifestyle interventions such as dietary patterns, antibiotics, and probiotics. In addition, choline utilization is also affected by genetic factors, further complicating the impact of choline on health. This review overviews the complex interplay between dietary intakes of choline, gut microbiota and genetic factors, and the subsequent impact on health. Understanding of gut microbiota metabolism of choline substrates and interindividual variability is warranted in the development of personalized choline nutrition.
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Affiliation(s)
- Ying Qi Goh
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
| | - Guoxiang Cheam
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
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25
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Krueger ES, Lloyd TS, Tessem JS. The Accumulation and Molecular Effects of Trimethylamine N-Oxide on Metabolic Tissues: It's Not All Bad. Nutrients 2021; 13:nu13082873. [PMID: 34445033 PMCID: PMC8400152 DOI: 10.3390/nu13082873] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Since elevated serum levels of trimethylamine N-oxide (TMAO) were first associated with increased risk of cardiovascular disease (CVD), TMAO research among chronic diseases has grown exponentially. We now know that serum TMAO accumulation begins with dietary choline metabolism across the microbiome-liver-kidney axis, which is typically dysregulated during pathogenesis. While CVD research links TMAO to atherosclerotic mechanisms in vascular tissue, its molecular effects on metabolic tissues are unclear. Here we report the current standing of TMAO research in metabolic disease contexts across relevant tissues including the liver, kidney, brain, adipose, and muscle. Since poor blood glucose management is a hallmark of metabolic diseases, we also explore the variable TMAO effects on insulin resistance and insulin production. Among metabolic tissues, hepatic TMAO research is the most common, whereas its effects on other tissues including the insulin producing pancreatic β-cells are largely unexplored. Studies on diseases including obesity, diabetes, liver diseases, chronic kidney disease, and cognitive diseases reveal that TMAO effects are unique under pathologic conditions compared to healthy controls. We conclude that molecular TMAO effects are highly context-dependent and call for further research to clarify the deleterious and beneficial molecular effects observed in metabolic disease research.
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Affiliation(s)
- Emily S. Krueger
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA; (E.S.K.); (T.S.L.)
| | - Trevor S. Lloyd
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA; (E.S.K.); (T.S.L.)
- Medical Education Program, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Jeffery S. Tessem
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA; (E.S.K.); (T.S.L.)
- Correspondence: ; Tel.: +1-801-422-9082
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26
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Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase. J Phys Chem B 2021; 125:7774-7784. [PMID: 34236200 DOI: 10.1021/acs.jpcb.1c05320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 2021; 10:65088. [PMID: 33944776 PMCID: PMC8096432 DOI: 10.7554/elife.65088] [Citation(s) in RCA: 674] [Impact Index Per Article: 224.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.
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Affiliation(s)
| | - Lauren J McIver
- Harvard T.H. Chan School of Public Health, Boston, United States
| | | | | | | | - Sagun Maharjan
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Ana Mailyan
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Matthias Scholz
- Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy
| | | | | | - George Weingart
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Yancong Zhang
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.,IEO, European Institute of Oncology IRCCS, Milan, Italy
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28
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Day-Walsh P, Shehata E, Saha S, Savva GM, Nemeckova B, Speranza J, Kellingray L, Narbad A, Kroon PA. The use of an in-vitro batch fermentation (human colon) model for investigating mechanisms of TMA production from choline, L-carnitine and related precursors by the human gut microbiota. Eur J Nutr 2021; 60:3987-3999. [PMID: 33934200 PMCID: PMC8437865 DOI: 10.1007/s00394-021-02572-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023]
Abstract
Purpose Plasma trimethylamine-N-oxide (TMAO) levels have been shown to correlate with increased risk of metabolic diseases including cardiovascular diseases. TMAO exposure predominantly occurs as a consequence of gut microbiota-dependent trimethylamine (TMA) production from dietary substrates including choline, carnitine and betaine, which is then converted to TMAO in the liver. Reducing microbial TMA production is likely to be the most effective and sustainable approach to overcoming TMAO burden in humans. Current models for studying microbial TMA production have numerous weaknesses including the cost and length of human studies, differences in TMA(O) metabolism in animal models and the risk of failing to replicate multi-enzyme/multi-strain pathways when using isolated bacterial strains. The purpose of this research was to investigate TMA production from dietary precursors in an in-vitro model of the human colon. Methods TMA production from choline, l-carnitine, betaine and γ-butyrobetaine was studied over 24–48 h using an in-vitro human colon model with metabolite quantification performed using LC–MS. Results Choline was metabolised via the direct choline TMA-lyase route but not the indirect choline–betaine-TMA route, conversion of l-carnitine to TMA was slower than that of choline and involves the formation of the intermediate γ-BB, whereas the Rieske-type monooxygenase/reductase pathway for l-carnitine metabolism to TMA was negligible. The rate of TMA production from precursors was choline > carnitine > betaine > γ-BB. 3,3-Dimethyl-1-butanol (DMB) had no effect on the conversion of choline to TMA. Conclusion The metabolic routes for microbial TMA production in the colon model are consistent with observations from human studies. Thus, this model is suitable for studying gut microbiota metabolism of TMA and for screening potential therapeutic targets that aim to attenuate TMA production by the gut microbiota. Trial registration number NCT02653001 (http://www.clinicaltrials.gov), registered 12 Jan 2016. Supplementary Information The online version contains supplementary material available at 10.1007/s00394-021-02572-6.
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Affiliation(s)
| | - Emad Shehata
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Chemistry of Flavour and Aroma Dept, National Research Centre, 33 El Buhouth St, Giza, 12622, Dokki, Egypt
| | - Shikha Saha
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Barbora Nemeckova
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Jasmine Speranza
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Foundation "Prof. Antonio Imbesi", University of Messina, Piazza Pugliatti 1, 98122, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
| | - Lee Kellingray
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Paul A Kroon
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
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29
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Cesle EE, Filimonenko A, Tars K, Kalnins G. Variety of size and form of GRM2 bacterial microcompartment particles. Protein Sci 2021; 30:1035-1043. [PMID: 33763934 PMCID: PMC8040866 DOI: 10.1002/pro.4069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi-permeable protein shell and an enzymatic core, they can enhance enzyme performance and protect the cell from harmful intermediates. With the ability to encapsulate non-native enzymes, BMCs show high potential for applied use. For this goal, a detailed look into shell form variability is significant to predict shell adaptability. Here we present four novel 3D cryo-EM maps of recombinant Klebsiella pneumoniae GRM2 BMC shell particles with the resolution in range of 9 to 22 Å and nine novel 2D classes corresponding to discrete BMC shell forms. These structures reveal icosahedral, elongated, oblate, multi-layered and polyhedral traits of BMCs, indicating considerable variation in size and form as well as adaptability during shell formation processes.
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Affiliation(s)
- Eva Emilija Cesle
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
| | - Anatolij Filimonenko
- CEITEC‐Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Kaspars Tars
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
- Faculty of BiologyUniversity of LatviaRigaLatvia
| | - Gints Kalnins
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
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30
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Iglesias-Carres L, Hughes MD, Steele CN, Ponder MA, Davy KP, Neilson AP. Use of dietary phytochemicals for inhibition of trimethylamine N-oxide formation. J Nutr Biochem 2021; 91:108600. [PMID: 33577949 DOI: 10.1016/j.jnutbio.2021.108600] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/01/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022]
Abstract
Trimethylamine-N-oxide (TMAO) has been reported as a risk factor for atherosclerosis development, as well as for other cardiovascular disease (CVD) pathologies. The objective of this review is to provide a useful summary on the use of phytochemicals as TMAO-reducing agents. This review discusses the main mechanisms by which TMAO promotes CVD, including the modulation of lipid and bile acid metabolism, and the promotion of endothelial dysfunction and oxidative stress. Current knowledge on the available strategies to reduce TMAO formation are discussed, highlighting the effect and potential of phytochemicals. Overall, phytochemicals (i.e., phenolic compounds or glucosinolates) reduce TMAO formation by modulating gut microbiota composition and/or function, inhibiting host's capacity to metabolize TMA to TMAO, or a combination of both. Perspectives for design of future studies involving phytochemicals as TMAO-reducing agents are discussed. Overall, the information provided by this review outlines the current state of the art of the role of phytochemicals as TMAO reducing agents, providing valuable insight to further advance in this field of study.
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Affiliation(s)
- Lisard Iglesias-Carres
- Department of Food, Bioprocessing and Nutrition Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC
| | - Michael D Hughes
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Cortney N Steele
- Department of Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Monica A Ponder
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Kevin P Davy
- Department of Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Andrew P Neilson
- Department of Food, Bioprocessing and Nutrition Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC.
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31
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Shanmugam M, Quareshy M, Cameron AD, Bugg TDH, Chen Y. Light-Activated Electron Transfer and Catalytic Mechanism of Carnitine Oxidation by Rieske-Type Oxygenase from Human Microbiota. Angew Chem Int Ed Engl 2020; 60:4529-4534. [PMID: 33180358 PMCID: PMC7986066 DOI: 10.1002/anie.202012381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Oxidation of quaternary ammonium substrate, carnitine by non‐heme iron containing Acinetobacter baumannii (Ab) oxygenase CntA/reductase CntB is implicated in the onset of human cardiovascular disease. Herein, we develop a blue‐light (365 nm) activation of NADH coupled to electron paramagnetic resonance (EPR) measurements to study electron transfer from the excited state of NADH to the oxidized, Rieske‐type, [2Fe‐2S]2+ cluster in the AbCntA oxygenase domain with and without the substrate, carnitine. Further electron transfer from one‐electron reduced, Rieske‐type [2Fe‐2S]1+ center in AbCntA‐WT to the mono‐nuclear, non‐heme iron center through the bridging glutamate E205 and subsequent catalysis occurs only in the presence of carnitine. The electron transfer process in the AbCntA‐E205A mutant is severely affected, which likely accounts for the significant loss of catalytic activity in the AbCntA‐E205A mutant. The NADH photo‐activation coupled with EPR is broadly applicable to trap reactive intermediates at low temperature and creates a new method to characterize elusive intermediates in multiple redox‐centre containing proteins.
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Affiliation(s)
- Muralidharan Shanmugam
- Manchester Institute of Biotechnology (MIB) & Photon Science Institute (PSI), University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Alexander D Cameron
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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32
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Shanmugam M, Quareshy M, Cameron AD, Bugg TDH, Chen Y. Light‐Activated Electron Transfer and Catalytic Mechanism of Carnitine Oxidation by Rieske‐Type Oxygenase from Human Microbiota. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Muralidharan Shanmugam
- Manchester Institute of Biotechnology (MIB) & Photon Science Institute (PSI) University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Mussa Quareshy
- School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Alexander D. Cameron
- School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Timothy D. H. Bugg
- Department of Chemistry University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Yin Chen
- School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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Gabr MT, Machalz D, Pach S, Wolber G. A benzoxazole derivative as an inhibitor of anaerobic choline metabolism by human gut microbiota. RSC Med Chem 2020; 11:1402-1412. [PMID: 34095847 PMCID: PMC8126876 DOI: 10.1039/d0md00218f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
Metabolic pathways mediated by human gut bacteria have emerged as potential therapeutic targets because of their association with the pathophysiology of various human diseases. The anaerobic transformation of choline into trimethylamine (TMA) by gut microbiota is directly linked to type 2 diabetes, fatty liver disease, and cardiovascular diseases. Structural analogs of choline have been developed as competitive inhibitors of choline TMA-lyase (CutC), a key enzyme for the conversion of choline to TMA. However, weak to moderate CutC inhibitory profiles of the choline analogs limit their further advancement into clinical translation. In this study, we introduce a glycomimetic-based approach for the identification of CutC inhibitors with intestinal metabolic stability. Our workflow started with screening of a small library of glycomimetics for metabolic stability in the presence of human intestinal S9 fraction. Further screening using an in vitro CutC inhibitory assay identified a benzoxazole ligand (BO-I) as a CutC inhibitor with an IC50 value of 2.4 ± 0.3 μM. Kinetic analysis revealed that BO-I functions as a non-competitive inhibitor of CutC. Interestingly, BO-I reduced the production of TMA in whole cell assays of multiple bacterial strains as well as in complex biological environments. Therefore, structural optimization of BO-I holds promise for the development of efficient gut microbiota-targeted small molecules.
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Affiliation(s)
- Moustafa T Gabr
- Department of Radiology, Stanford University School of Medicine Stanford CA 94305 USA
| | - David Machalz
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design) Berlin Germany
| | - Szymon Pach
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design) Berlin Germany
| | - Gerhard Wolber
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design) Berlin Germany
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Gabr M, Świderek K. Discovery of a Histidine-Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine-Lyase. ChemMedChem 2020; 15:2273-2279. [PMID: 32827245 DOI: 10.1002/cmdc.202000571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 01/07/2023]
Abstract
Anaerobic choline metabolism by human gut microbiota to produce trimethylamine (TMA) has recently evolved as a potential therapeutic target because of its association with chronic kidney disease and increased cardiovascular risks. Limited examples of choline analogues have been reported as inhibitors of bacterial enzyme choline TMA-lyase (CutC), a key enzyme regulating choline anaerobic metabolism. We used a new workflow to discover CutC inhibitors based on focused screening of a diversified library of small molecules for intestinal metabolic stability followed by in vitro CutC inhibitory assay. This workflow identified a histidine-based scaffold as a CutC inhibitor with an IC50 value of 1.9±0.2 μM. Remarkably, the identified CutC inhibitor was able to reduce the production of TMA in whole-cell assays using various bacterial strains as well as in complex gut microbiota environment. The improved efficiency of the new scaffold identified in this study in comparison to previously reported CutC inhibitors would enable optimization of potential leads for in vivo screening and clinical translation. Finally, docking studies and molecular-dynamic simulations were used to predict putative interactions created between inhibitor and CutC.
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Affiliation(s)
- Moustafa Gabr
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castellón, Spain
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35
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Quareshy M, Shanmugam M, Townsend E, Jameson E, Bugg TDH, Cameron AD, Chen Y. Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer. J Biol Chem 2020; 296:100038. [PMID: 33158989 PMCID: PMC7948474 DOI: 10.1074/jbc.ra120.016019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial metabolism of carnitine to trimethylamine (TMA) in the gut can accelerate atherosclerosis and heart disease, and these TMA-producing enzymes are therefore important drug targets. Here, we report the first structures of the carnitine oxygenase CntA, an enzyme of the Rieske oxygenase family. CntA exists in a head-to-tail α3 trimeric structure. The two functional domains (the Rieske and the catalytic mononuclear iron domains) are located >40 Å apart in the same monomer but adjacent in two neighboring monomers. Structural determination of CntA and subsequent electron paramagnetic resonance measurements uncover the molecular basis of the so-called bridging glutamate (E205) residue in intersubunit electron transfer. The structures of the substrate-bound CntA help to define the substrate pocket. Importantly, a tyrosine residue (Y203) is essential for ligand recognition through a π-cation interaction with the quaternary ammonium group. This interaction between an aromatic residue and quaternary amine substrates allows us to delineate a subgroup of Rieske oxygenases (group V) from the prototype ring-hydroxylating Rieske oxygenases involved in bioremediation of aromatic pollutants in the environment. Furthermore, we report the discovery of the first known CntA inhibitors and solve the structure of CntA in complex with the inhibitor, demonstrating the pivotal role of Y203 through a π-π stacking interaction with the inhibitor. Our study provides the structural and molecular basis for future discovery of drugs targeting this TMA-producing enzyme in human gut.
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Affiliation(s)
- Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology & Photon Science Institute, The University of Manchester, Manchester, UK
| | | | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK.
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Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
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Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
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Pretorius L, Smith C. The trace aminergic system: a gender-sensitive therapeutic target for IBS? J Biomed Sci 2020; 27:95. [PMID: 32981524 PMCID: PMC7520957 DOI: 10.1186/s12929-020-00688-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Due to a lack of specific or sensitive biomarkers, drug discovery advances have been limited for individuals suffering from irritable bowel syndrome (IBS). While current therapies provide symptomatic relief, inflammation itself is relatively neglected, despite the presence of chronic immune activation and innate immune system dysfunction. Moreover, considering the microgenderome concept, gender is a significant aetiological risk factor. We believe that we have pinpointed a "missing link" that connects gender, dysbiosis, diet, and inflammation in the context of IBS, which may be manipulated as therapeutic target. The trace aminergic system is conveniently positioned at the interface of the gut microbiome, dietary nutrients and by-products, and mucosal immunity. Almost all leukocyte populations express trace amine associated receptors and significant amounts of trace amines originate from both food and the gut microbiota. Additionally, although IBS-specific data are sparse, existing data supports an interpretation in favour of a gender dependence in trace aminergic signalling. As such, trace aminergic signalling may be altered by fluctuations of especially female reproductive hormones. Utilizing a multidisciplinary approach, this review discusses potential mechanisms of actions, which include hyperreactivity of the immune system and aberrant serotonin signalling, and links outcomes to the symptomology clinically prevalent in IBS. Taken together, it is feasible that the additional level of regulation by the trace aminergic system in IBS has been overlooked, until now. As such, we suggest that components of the trace aminergic system be considered targets for future therapeutic action, with the specific focus of reducing oxidative stress and inflammation.
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Affiliation(s)
- Lesha Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Stellenbosch, 7062, South Africa
| | - Carine Smith
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Stellenbosch, 7062, South Africa.
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Metformin decreases bacterial trimethylamine production and trimethylamine N-oxide levels in db/db mice. Sci Rep 2020; 10:14555. [PMID: 32884086 PMCID: PMC7471276 DOI: 10.1038/s41598-020-71470-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
The current study aimed to explore whether metformin, the most widely prescribed oral medication for the treatment of type 2 diabetes, alters plasma levels of cardiometabolic disease-related metabolite trimethylamine N-oxide (TMAO) in db/db mice with type 2 diabetes. TMAO plasma concentration was up to 13.2-fold higher in db/db mice when compared to control mice, while in db/db mice fed choline-enriched diet, that mimics meat and dairy product intake, TMAO plasma level was increased 16.8-times. Metformin (250 mg/kg/day) significantly decreased TMAO concentration by up to twofold in both standard and choline-supplemented diet-fed db/db mice plasma. In vitro, metformin significantly decreased the bacterial production rate of trimethylamine (TMA), the precursor of TMAO, from choline up to 3.25-fold in K. pneumoniae and up to 26-fold in P. Mirabilis, while significantly slowing the growth of P. Mirabilis only. Metformin did not affect the expression of genes encoding subunits of bacterial choline-TMA-lyase microcompartment, the activity of the enzyme itself and choline uptake, suggesting that more complex regulation beyond the choline-TMA-lyase is present. To conclude, the TMAO decreasing effect of metformin could be an additional mechanism behind the clinically observed cardiovascular benefits of the drug.
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Gabr MT, Deganutti G, Reynolds CA. Peptidomimetic-based approach toward inhibitors of microbial trimethylamine lyases. Chem Biol Drug Des 2020; 97:231-236. [PMID: 32772476 DOI: 10.1111/cbdd.13775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/27/2020] [Accepted: 08/01/2020] [Indexed: 12/30/2022]
Abstract
The development of gut microbiota-targeted small molecules represents a promising platform for the identification of new therapeutics based on the implication of human gut bacteria with different diseases. Bacterial trimethylamine (TMA)-lyase (CutC) is expressed in gut bacteria and catalyzes the conversion of choline to TMA. The association of elevated TMA production with various disorders has directed research efforts toward identification of CutC inhibitors. Herein, we introduce peptidomimetics as a promising toolbox for the discovery of CutC inhibitors. Our approach starts with screening a library of peptidomimetics for intestinal metabolic stability followed by in vitro CutC inhibition. Compound 5 was identified from this screening platform with IC50 value of 5.9 ± 0.6 μM for CutC inhibition. Unlike previously reported CutC inhibitors, compound 5 possessed universal CutC inhibitory activity in different bacterial strains. Molecular dynamics simulations suggested a plausible binding site and inhibition mechanism for compound 5. Therefore, compound 5 is a promising lead for further structural optimization in the search for CutC-targeted small molecules.
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Affiliation(s)
- Moustafa T Gabr
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
| | - Christopher A Reynolds
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
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40
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Gut metagenomic and short chain fatty acids signature in hypertension: a cross-sectional study. Sci Rep 2020; 10:6436. [PMID: 32296109 PMCID: PMC7160119 DOI: 10.1038/s41598-020-63475-w] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 03/24/2020] [Indexed: 01/05/2023] Open
Abstract
Hypertension is an independent and preventable risk factor for the development of cardiovascular diseases, however, little is known about the impact of gut microbiota composition in its development. We carried out comprehensive gut microbiota analysis and targeted metabolomics in a cross-sectional study of 29 non-treated hypertensive (HT) and 32 normotensive (NT) subjects. We determined fecal microbiota composition by 16S rRNA gene sequencing and bacterial functions by metagenomic analysis. The microbial metabolites analysed were short chain fatty acids (SCFA) both in plasma and feces, and trimethylamine N-oxide (TMAO) in plasma. The overall bacterial composition and diversity of bacterial community in the two groups were not significantly different. However, Ruminococcaceae NK4A214, Ruminococcaceae_UCG-010, Christensenellaceae_R-7, Faecalibacterium prausnitzii and Roseburia hominis were found to be significantly enriched in NT group, whereas, Bacteroides coprocola, Bacteroides plebeius and genera of Lachnospiraceae were increased in HT patients. We found a positive correlation between the HT-associated species and systolic and diastolic blood pressure after adjusted for measured confounders. SCFA showed antagonistic results in plasma and feces, detecting in HT subjects significant higher levels in feces and lower levels in plasma, which could indicate a less efficient SCFA absorption. Overall, our results present a disease classifier based on microbiota and bacterial metabolites to discriminate HT individuals from NT controls in a first disease grade prior to drug treatment.
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41
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Backman LRF, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL. Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. eLife 2020; 9:e51420. [PMID: 32180548 PMCID: PMC7077986 DOI: 10.7554/elife.51420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/19/2020] [Indexed: 02/04/2023] Open
Abstract
The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.
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Affiliation(s)
- Lindsey RF Backman
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yolanda Y Huang
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Mary C Andorfer
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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Rodrigues AV, Tantillo DJ, Mukhopadhyay A, Keasling JD, Beller HR. Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme. Chembiochem 2020; 21:663-671. [PMID: 31512343 PMCID: PMC7079210 DOI: 10.1002/cbic.201900560] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Indexed: 01/14/2023]
Abstract
We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting the formidable demands on PhdB for catalysis of this reaction. Evidence that PhdB was able to bind α,α-difluorophenylacetate but was unable to catalyze its decarboxylation supported the enzyme's abstraction of a methylene H atom. Diminished activity of H327A and Y691F mutants was consistent with proposed proton donor roles for His327 and Tyr691. Collectively, these and other data most strongly support PhdB attack at the methylene carbon.
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Affiliation(s)
- Andria V. Rodrigues
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California1 Shields AvenueDavisCA95616USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Department of BioengineeringUniversity of California306 Stanley HallBerkeleyCA94720USA
- Department of Chemical and Biomolecular EngineeringUniversity of California201 Gilman HallBerkeleyCA94720USA
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkBuilding 220, Kemitorvet2800Kgs. LyngbyDenmark
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
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Kalnins G, Cesle EE, Jansons J, Liepins J, Filimonenko A, Tars K. Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Nat Commun 2020; 11:388. [PMID: 31959751 PMCID: PMC6971018 DOI: 10.1038/s41467-019-14205-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/18/2019] [Indexed: 11/08/2022] Open
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia.
| | - Eva-Emilija Cesle
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Anatolij Filimonenko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas 1, Riga, 1004, Latvia
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Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene ( cutC) Harbored by Enterobacteriaceae. Nutrients 2019; 12:nu12010062. [PMID: 31881690 PMCID: PMC7019844 DOI: 10.3390/nu12010062] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Gut microbiota metabolization of dietary choline may promote atherosclerosis through trimethylamine (TMA), which is rapidly absorbed and converted in the liver to proatherogenic trimethylamine-N-oxide (TMAO). The aim of this study was to verify whether TMAO urinary levels may be associated with the fecal relative abundance of specific bacterial taxa and the bacterial choline TMA-lyase gene cutC. The analysis of sequences available in GenBank grouped the cutC gene into two main clusters, cut-Dd and cut-Kp. A quantitative real-time polymerase chain reaction (qPCR) protocol was developed to quantify cutC and was used with DNA isolated from three fecal samples collected weekly over the course of three consecutive weeks from 16 healthy adults. The same DNA was used for 16S rRNA gene profiling. Concomitantly, urine was used to quantify TMAO by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). All samples were positive for cutC and TMAO. Correlation analysis showed that the cut-Kp gene cluster was significantly associated with Enterobacteriaceae. Linear mixed models revealed that urinary TMAO levels may be predicted by fecal cut-Kp and by 23 operational taxonomic units (OTUs). Most of the OTUs significantly associated with TMAO were also significantly associated with cut-Kp, confirming the possible relationship between these two factors. In conclusion, this preliminary method-development study suggests the existence of a relationship between TMAO excreted in urine, specific fecal bacterial OTUs, and a cutC subgroup ascribable to the choline-TMA conversion enzymes of Enterobacteriaceae.
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45
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Wishart DS. Metabolomics for Investigating Physiological and Pathophysiological Processes. Physiol Rev 2019; 99:1819-1875. [PMID: 31434538 DOI: 10.1152/physrev.00035.2018] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry techniques to enable the high-throughput characterization of metabolites from cells, organs, tissues, or biofluids. The rapid growth in metabolomics is leading to a renewed interest in metabolism and the role that small molecule metabolites play in many biological processes. As a result, traditional views of metabolites as being simply the "bricks and mortar" of cells or just the fuel for cellular energetics are being upended. Indeed, metabolites appear to have much more varied and far more important roles as signaling molecules, immune modulators, endogenous toxins, and environmental sensors. This review explores how metabolomics is yielding important new insights into a number of important biological and physiological processes. In particular, a major focus is on illustrating how metabolomics and discoveries made through metabolomics are improving our understanding of both normal physiology and the pathophysiology of many diseases. These discoveries are yielding new insights into how metabolites influence organ function, immune function, nutrient sensing, and gut physiology. Collectively, this work is leading to a much more unified and system-wide perspective of biology wherein metabolites, proteins, and genes are understood to interact synergistically to modify the actions and functions of organelles, organs, and organisms.
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Affiliation(s)
- David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
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46
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Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat Med 2019; 25:667-678. [PMID: 30936548 PMCID: PMC9533319 DOI: 10.1038/s41591-019-0405-7] [Citation(s) in RCA: 443] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023]
Abstract
Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers across cohorts and populations. We performed a meta-analysis of five publicly available datasets and two new cohorts and validated the findings on two additional cohorts, considering in total 969 fecal metagenomes. Unlike microbiome shifts associated with gastrointestinal syndromes, the gut microbiome in CRC showed reproducibly higher richness than controls (P < 0.01), partially due to expansions of species typically derived from the oral cavity. Meta-analysis of the microbiome functional potential identified gluconeogenesis and the putrefaction and fermentation pathways as being associated with CRC, whereas the stachyose and starch degradation pathways were associated with controls. Predictive microbiome signatures for CRC trained on multiple datasets showed consistently high accuracy in datasets not considered for model training and independent validation cohorts (average area under the curve, 0.84). Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase gene was overabundant in CRC (P = 0.001), identifying a relationship between microbiome choline metabolism and CRC. The combined analysis of heterogeneous CRC cohorts thus identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.
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Affiliation(s)
- Andrew Maltez Thomas
- Department CIBIO, University of Trento, Trento, Italy
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, Brazil
- Medical Genomics Laboratory, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Chiara Pozzi
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Sara Gandini
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Sonia Tarallo
- Italian Institute for Genomic Medicine, Turin, Italy
| | | | - Gaetano Gallo
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
- Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy
| | - Mario Trompetto
- Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy
| | - Giulio Ferrero
- Department of Computer Science, University of Turin, Turin, Italy
| | - Sayaka Mizutani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hirotsugu Shiroma
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Satoshi Shiba
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinichi Yachida
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Cancer Genome Informatics, Osaka University, Osaka, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Hermann Brenner
- Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Healthy Sciences, University of Southern Denmark, Odense, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Emmanuel Dias-Neto
- Medical Genomics Laboratory, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
- Laboratory of Neurosciences, Institute of Psychiatry, University of São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, Brazil
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Maria Rescigno
- Mucosal Immunology and Microbiota Unit, Humanitas Research Hospital, Milan, Italy
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
- Institute for Implementation Science in Population Health, City University of New York, New York, NY, USA
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine, Turin, Italy
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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Nilsson Å, Duan RD. Pancreatic and mucosal enzymes in choline phospholipid digestion. Am J Physiol Gastrointest Liver Physiol 2019; 316:G425-G445. [PMID: 30576217 DOI: 10.1152/ajpgi.00320.2018] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The digestion of choline phospholipids is important for choline homeostasis, lipid signaling, postprandial lipid and energy metabolism, and interaction with intestinal bacteria. The digestion is mediated by the combined action of pancreatic and mucosal enzymes. In the proximal small intestine, hydrolysis of phosphatidylcholine (PC) to 1-lyso-PC and free fatty acid (FFA) by the pancreatic phospholipase A2 IB coincides with the digestion of the dietary triacylglycerols by lipases, but part of the PC digestion is extended and must be mediated by other enzymes as the jejunoileal brush-border phospholipase B/lipase and mucosal secreted phospholipase A2 X. Absorbed 1-lyso-PC is partitioned in the mucosal cells between degradation and reacylation into chyle PC. Reutilization of choline for hepatic bile PC synthesis, and the reacylation of 1-lyso-PC into chylomicron PC by the lyso-PC-acyl-CoA-acyltransferase 3 are important features of choline recycling and postprandial lipid metabolism. The role of mucosal enzymes is emphasized by sphingomyelin (SM) being sequentially hydrolyzed by brush-border alkaline sphingomyelinase (alk-SMase) and neutral ceramidase to sphingosine and FFA, which are well absorbed. Ceramide and sphingosine-1-phosphate are generated and are both metabolic intermediates and important lipid messengers. Alk-SMase has anti-inflammatory effects that counteract gut inflammation and tumorigenesis. These may be mediated by multiple mechanisms including generation of sphingolipid metabolites and suppression of autotaxin induction and lyso-phosphatidic acid formation. Here we summarize current knowledge on the roles of pancreatic and mucosal enzymes in PC and SM digestion, and its implications in intestinal and liver diseases, bacterial choline metabolism in the gut, and cholesterol absorption.
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Affiliation(s)
- Åke Nilsson
- Department of Clow-linical Sciences Lund, Division of Medicine, Gastroenterology, Lund University , Lund , Sweden
| | - Rui-Dong Duan
- Gastroenterology and Nutrition Laboratory, Department of Clinical Sciences, Lund University , Lund , Sweden
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48
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Yang Z, Mehmood R, Wang M, Qi HW, Steeves AH, Kulik HJ. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. REACT CHEM ENG 2019; 4:298-315. [PMID: 31572618 PMCID: PMC6768422 DOI: 10.1039/c8re00213d] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mengyi Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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Ferlez B, Sutter M, Kerfeld CA. Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles. mBio 2019; 10:e02327-18. [PMID: 30622187 PMCID: PMC6325248 DOI: 10.1128/mbio.02327-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
An increasing number of microbes are being identified that organize catabolic pathways within self-assembling proteinaceous structures known as bacterial microcompartments (BMCs). Most BMCs are characterized by their singular substrate specificity and commonly employ B12-dependent radical mechanisms. In contrast, a less-well-known BMC type utilizes the B12-independent radical chemistry of glycyl radical enzymes (GREs). Unlike B12-dependent enzymes, GREs require an activating enzyme (AE) as well as an external source of electrons to generate an adenosyl radical and form their catalytic glycyl radical. Organisms encoding these glycyl radical enzyme-associated microcompartments (GRMs) confront the challenge of coordinating the activation and maintenance of their GREs with the assembly of a multienzyme core that is encapsulated in a protein shell. The GRMs appear to enlist redox proteins to either generate reductants internally or facilitate the transfer of electrons from the cytosol across the shell. Despite this relative complexity, GRMs are one of the most widespread types of BMC, with distinct subtypes to catabolize different substrates. Moreover, they are encoded by many prominent gut-associated and pathogenic bacteria. In this review, we will focus on the diversity, function, and physiological importance of GRMs, with particular attention given to their associated and enigmatic redox proteins.
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Affiliation(s)
- Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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50
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Wang F, Xu J, Jakovlić I, Wang WM, Zhao YH. Dietary betaine reduces liver lipid accumulationviaimprovement of bile acid and trimethylamine-N-oxide metabolism in blunt-snout bream. Food Funct 2019; 10:6675-6689. [DOI: 10.1039/c9fo01853k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dietary betaine decreased liver lipid accumulation caused by dietary carbohydrate through changes of TMA formation and TMAO and bile acid metabolism.
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Affiliation(s)
- Fan Wang
- College of Fisheries Huazhong Agricultural University
- Key Lab of Freshwater Animal Breeding
- Ministry of Agriculture
- Key Lab of Agricultural Animal Genetics
- Breeding and Reproduction of Ministry of Education
| | - Jia Xu
- College of Fisheries Huazhong Agricultural University
- Key Lab of Freshwater Animal Breeding
- Ministry of Agriculture
- Key Lab of Agricultural Animal Genetics
- Breeding and Reproduction of Ministry of Education
| | | | - Wei-Min Wang
- College of Fisheries Huazhong Agricultural University
- Key Lab of Freshwater Animal Breeding
- Ministry of Agriculture
- Key Lab of Agricultural Animal Genetics
- Breeding and Reproduction of Ministry of Education
| | - Yu-Hua Zhao
- College of Fisheries Huazhong Agricultural University
- Key Lab of Freshwater Animal Breeding
- Ministry of Agriculture
- Key Lab of Agricultural Animal Genetics
- Breeding and Reproduction of Ministry of Education
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