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Goc A, Sumera W, Rath M, Niedzwiecki A. Antibacterial and Antibiofilm Effects of L-Carnitine-Fumarate on Oral Streptococcal Strains Streptococcus mutans and Streptococcus sobrinus. Microorganisms 2024; 12:1613. [PMID: 39203455 PMCID: PMC11356751 DOI: 10.3390/microorganisms12081613] [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: 07/15/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 09/03/2024] Open
Abstract
Streptococcus mutans is a major pathogenic habitant of oral caries. Owing to its physiological and biochemical features, it prevails in the form of plaque biofilm together with another important mutans streptococci species, Streptococcus sobrinus. Both species are considered as initiators of cavity lesions, and biofilm is essential to the dental caries process. Compared with the planktonic populations, the biofilm form has higher resistance to environmental conditions and antibiotics. Dental plaques also secure the long-term survival of microorganisms and protection from any stress conditions. To address the need for new antibiofilm agents, we have focused on L-carnitine-fumarate, a fumarate-conjugated quaternary ammonium compound. Using the macro-broth susceptibility testing method, we established its MIC value as 6.0 mg/mL. The MBC value, determined from the broth dilution minimum inhibitory concentration test by sub-culturing it to BHI agar plates, was established as 7.0 mg/mL. Antibiofilm efficacy was tested in 96-well plates coated with saliva using BHI broth supplemented with 1% sucrose as a standard approach. The obtained results allowed us to assess the MIBC as 7.5 mg/mL and the MBBC value as 10.0 mg/mL. The latter concentration also caused approximately 20% eradication of pre-existing biofilm. EPS-rich matrix, forming the core of the biofilm and enabling a confined acidic microenvironment, was also examined and confirmed the effectiveness of 10.0 mg/mL L-carnitine-fumarate concentration in inhibiting EPS formation. Furthermore, the anti-adherent and anti-aciduric impacts of L-carnitine-fumarate were investigated and revealed significant inhibitory effects at sub-MIC concentrations. The influence of L-carnitine-fumarate on the phosphotransferase system was investigated as well. Our results provide a new insight into the antibacterial potential of L-carnitine-fumarate as a valuable compound to be considered for alternative or adjunct anti-caries and antibiofilm preventive approaches.
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Affiliation(s)
- Anna Goc
- Dr. Rath Research Institute, 5941 Optical Ct., San Jose, CA 95138, USA; (W.S.); (M.R.)
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2
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Eyheraguibel B, Diémé B, Lagrée M, Durand S, Barbe V, Meistertzheim AL, Ter Halle A, Burgaud G, Ghiglione JF. Untargeted metabolomic insights into plastisphere communities in European rivers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34214-9. [PMID: 39090296 DOI: 10.1007/s11356-024-34214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/29/2024] [Indexed: 08/04/2024]
Abstract
Every year, rivers introduce a staggering amount of hundred kilotons of plastic into the Oceans. This plastic is inhabited by microorganisms known as the plastisphere, which can be transferred between different ecosystems through the transport of microplastics. Here, we simulated the microbial colonization of polyethylene-based plastic pellets that are classically used to manufacture large-scale plastic products. The pellets were immersed for 1 month in four to five sampling stations along the river-to-sea continuum of nine of the major European rivers. This study presents the first untargeted metabolomics analysis of the plastisphere, by using ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS). The plastisphere metabolomes were similar in the Rhine and Rhone rivers, while being different from the Tiber and Loire rivers, which showed greater similarity to the Thames and Seine rivers. Interestingly, we found a clear distinction between plastisphere metabolomes from freshwater and marine water in most of the river-to-sea continuum, thus suggesting a complete segregation in plastisphere metabolites that is not consistent with a major transfer of microorganisms between the two contrasted ecosystems. Putative annotations of 189 discriminating metabolites suggested that lipid metabolism was significantly modulated. These results enlightened the relevance of using environmental metabolomic as complementary analysis to the current OMICs analysis.
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Affiliation(s)
- Boris Eyheraguibel
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6296, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Binta Diémé
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marie Lagrée
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Stéphanie Durand
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Alexandra Ter Halle
- Laboratoire Softmat, Université de Toulouse, Université Toulouse III - Paul Sabatier, CNRS UMR 5623, Toulouse, France
| | - Gaétan Burgaud
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Univ Brest, INRAE, Plouzané, France
| | - Jean-François Ghiglione
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, UMR 7621, Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
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Liu Y, Zhang F, Hawkins JL, Elder JR, Baranzoni GM, Huang Z, Fratamico PM, Parveen S. Comparative Gene Expression Analysis of Salmonella Typhimurium DT104 in Ground Chicken Extract and Brain Heart Infusion Broth. Microorganisms 2024; 12:1461. [PMID: 39065229 PMCID: PMC11279075 DOI: 10.3390/microorganisms12071461] [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: 07/03/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Salmonella enterica Typhimurium DT104 (S. Typhimurium DT104) is an important foodborne pathogen that is associated with poultry and poultry products. Currently, there is very little information on the underlying molecular mechanisms that allow DT104 to survive and propagate in poultry meat and the poultry processing environment. The current study assessed the global gene expression of DT104 in ground chicken extract (GCE) compared to brain heart infusion (BHI) medium using RNA-Seq technology. DT104 was grown to the early stationary phase (ESP), inoculated into GCE or BHI, and then re-grown to the log phase before RNA was extracted and transcripts were quantified by RNA-Seq. Gene expression for DT104 grown in GCE was then compared to that of DT104 grown in BHI for samples grown to the ESP. Growth in GCE resulted in the up-regulated expression of genes related to translation, carnitine metabolism (23-283-fold change), and cobalamin (vitamin B12) biosynthesis (14-fold change). In particular, the presence of carnitine in chicken meat, and thus, in GCE, which lacks carbohydrates, may allow Salmonella to utilize this compound as a carbon and nitrogen source. This study demonstrates that RNA-Seq data can provide a comprehensive analysis of DT104 gene expression in a food model for poultry products. This study also provides additional evidence for the importance of metabolic adaptation in the ability of S. enterica to successfully adapt to and occupy niches outside of its host and provides potential targets that could be used to develop intervention strategies to control Salmonella in poultry.
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Affiliation(s)
- Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Fangyuan Zhang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA
| | - Jabari L. Hawkins
- Food and Agricultural Sciences Graduate Program, Food and Resource Sciences, U.S. Department of Agriculture, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Jake R. Elder
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Gian Marco Baranzoni
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA
| | - Pina M. Fratamico
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Salina Parveen
- Food and Agricultural Sciences Graduate Program, Food and Resource Sciences, U.S. Department of Agriculture, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
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Samodelov SL, Gai Z, De Luca F, Haldimann K, Hobbie SN, Müller D, Kullak-Ublick GA, Visentin M. L-carnitine co-administration prevents colistin-induced mitochondrial permeability transition and reduces the risk of acute kidney injury in mice. Sci Rep 2024; 14:16444. [PMID: 39013979 PMCID: PMC11252255 DOI: 10.1038/s41598-024-67171-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Colistin is a polymyxin antibiotic currently experiencing renewed clinical interest due to its efficacy in the treatment of multidrug resistant (MDR) bacterial infections. The frequent onset of acute dose-dependent kidney injury, with the potential of leading to long-term renal damage, has limited its use and hampered adequate dosing regimens, increasing the risk of suboptimal plasma concentrations during treatment. The mechanism of colistin-induced renal toxicity has been postulated to stem from mitochondrial damage, yet there is no direct evidence of colistin acting as a mitochondrial toxin. The aim of this study was to evaluate whether colistin can directly induce mitochondrial toxicity and, if so, uncover the underlying molecular mechanism. We found that colistin leads to a rapid permeability transition of mitochondria isolated from mouse kidney that was fully prevented by co-incubation of the mitochondria with desensitizers of the mitochondrial transition pore cyclosporin A or L-carnitine. The protective effect of L-carnitine was confirmed in experiments in primary cultured mouse tubular cells. Consistently, the relative risk of colistin-induced kidney damage, calculated based on histological analysis as well as by the early marker of tubular kidney injury, Kim-1, was halved under co-administration with L-carnitine in vivo. Notably, L-carnitine neither affected the pharmacokinetics of colistin nor its antimicrobial activity against relevant bacterial strains. In conclusion, colistin targets the mitochondria and induces permeability transition thereof. L-carnitine prevents colistin-induced permeability transition in vitro. Moreover, L-carnitine co-administration confers partial nephroprotection in mice treated with colistin, without interfering with its pharmacokinetics and antibacterial activity.
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Affiliation(s)
- Sophia L Samodelov
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of Zürich, 8006, Zürich, Switzerland
| | - Zhibo Gai
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of Zürich, 8006, Zürich, Switzerland
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Francesca De Luca
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of Zürich, 8006, Zürich, Switzerland
| | - Klara Haldimann
- Institute of Medical Microbiology, University of Zürich, 8006, Zürich, Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zürich, 8006, Zürich, Switzerland
| | - Daniel Müller
- Institute of Clinical Chemistry, University Hospital Zürich, University of Zürich, 8006, Zürich, Switzerland
- Laboratory Medicine, University of Basel, 4056, Basel, Switzerland
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of Zürich, 8006, Zürich, Switzerland
- Mechanistic Safety, Patient Safety & Pharmacovigilance, Clinical Development and Medical Affairs, Novartis Pharma, 4056, Basel, Switzerland
| | - Michele Visentin
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of Zürich, 8006, Zürich, Switzerland.
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Brunetti AE, Lyra ML, Bauermeister A, Bunk B, Boedeker C, Müsken M, Neto FC, Mendonça JN, Caraballo-Rodríguez AM, Melo WG, Pupo MT, Haddad CF, Cabrera GM, Overmann J, Lopes NP. Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome. iScience 2023; 26:108109. [PMID: 37867936 PMCID: PMC10587524 DOI: 10.1016/j.isci.2023.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/23/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023] Open
Abstract
The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts' health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs' skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs' skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs' multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.
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Affiliation(s)
- Andrés E. Brunetti
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones N3300LQH, Argentina
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Straße 8, 07745 Jena, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi 129188, United Arab Emirates
| | - Anelize Bauermeister
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Christian Boedeker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Niedersachsen, Germany
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Jacqueline Nakau Mendonça
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Weilan G.P. Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Mônica T. Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Célio F.B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Gabriela M. Cabrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos aplicados a la Química Orgánica (UMYMFOR), Buenos Aires C1428EGA, Argentina
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Norberto P. Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
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6
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Lemons JMS, Conrad M, Tanes C, Chen J, Friedman ES, Roggiani M, Curry D, Chau L, Hecht AL, Harling L, Vales J, Kachelries KE, Baldassano RN, Goulian M, Bittinger K, Master SR, Liu L, Wu GD. Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 17:131-148. [PMID: 37739064 PMCID: PMC10694575 DOI: 10.1016/j.jcmgh.2023.09.005] [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: 05/02/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND & AIMS Altered plasma acylcarnitine levels are well-known biomarkers for a variety of mitochondrial fatty acid oxidation disorders and can be used as an alternative energy source for the intestinal epithelium when short-chain fatty acids are low. These membrane-permeable fatty acid intermediates are excreted into the gut lumen via bile and are increased in the feces of patients with inflammatory bowel disease (IBD). METHODS Herein, based on studies in human subjects, animal models, and bacterial cultures, we show a strong positive correlation between fecal carnitine and acylcarnitines and the abundance of Enterobacteriaceae in IBD where they can be consumed by bacteria both in vitro and in vivo. RESULTS Carnitine metabolism promotes the growth of Escherichia coli via anaerobic respiration dependent on the cai operon, and acetylcarnitine dietary supplementation increases fecal carnitine levels with enhanced intestinal colonization of the enteric pathogen Citrobacter rodentium. CONCLUSIONS In total, these results indicate that the increased luminal concentrations of carnitine and acylcarnitines in patients with IBD may promote the expansion of pathobionts belonging to the Enterobacteriaceae family, thereby contributing to disease pathogenesis.
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Affiliation(s)
- Johanna M S Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania
| | - Maire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jie Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elliot S Friedman
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dylan Curry
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lillian Chau
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aaron L Hecht
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lisa Harling
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer Vales
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly E Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania.
| | - Gary D Wu
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Role of carnitine in adaptation of Chromohalobacter salexigens DSM 3043 and its mutants to osmotic and temperature stress in defined medium. Extremophiles 2022; 26:28. [DOI: 10.1007/s00792-022-01276-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022]
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Martín A, Giráldez FJ, Cremonesi P, Castiglioni B, Biscarini F, Ceciliani F, Santos N, Andrés S. Dietary Administration of L-Carnitine During the Fattening Period of Early Feed Restricted Lambs Modifies Ruminal Fermentation but Does Not Improve Feed Efficiency. Front Physiol 2022; 13:840065. [PMID: 35309073 PMCID: PMC8929275 DOI: 10.3389/fphys.2022.840065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Early feed restriction of lambs may program animals to achieve reduced feed efficiency traits as a consequence of permanent mitochondrial dysfunction. The hypothesis at the background of the present study is that dietary administration of L-Carnitine (a compound that promotes the activation and transportation of fatty acids into the mitochondria) during the fattening period of early feed restricted lambs can: (a) improve the biochemical profile of early feed restricted lambs, (b) improve feed efficiency, (c) modulate the ruminal and intestinal microbiota, and (d) induce changes in the gastrointestinal mucosa, including the immune status. Twenty-two newborn male Merino lambs were raised under natural conditions but separated from the dams for 9 h daily to allow feed restriction during the suckling period. At weaning, lambs were assigned to a control group being fed ad libitum a complete pelleted diet during the fattening phase (CTRL, n = 11), whereas the second group (CARN, n = 11) received the same diet supplemented with 3 g of L-Carnitine/kg diet. The results revealed that even though L-Carnitine was absorbed, feed efficiency was not modified by dietary L-Carnitine during the fattening period (residual feed intake, p > 0.05), whereas ruminal fermentation was improved [total short-chain fatty acids (SCFAs), 113 vs. 154 mmol/l; p = 0.036]. Moreover, a trend toward increased concentration of butyrate in the ileal content (0.568 vs. 1.194 mmol/100 ml SCFA; p = 0.074) was observed. Other effects, such as reduced heart weight, lower levels of markers related to muscle metabolism or damage, improved renal function, and increased ureagenesis, were detected in the CARN group. Limited changes in the microbiota were also detected. These findings suggest that L-Carnitine may improve ruminal fermentation parameters and maintain both the balance of gut microbiota and the health of the animals. However, the improved ruminal fermentation and the consequent greater accumulation of intramuscular fat might have hidden the effects caused by the ability of dietary L-Carnitine to increase fatty acid oxidation at the mitochondrial level. This would explain the lack of effects of L-Carnitine supplementation on feed efficiency and points toward the need of testing lower doses, probably in the context of animals being fed in excess non-protein nitrogen.
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Affiliation(s)
- Alba Martín
- Department of Nutrition and Production of Herbivores, Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - F. Javier Giráldez
- Department of Nutrition and Production of Herbivores, Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Lodi, Italy
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Lodi, Italy
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Lodi, Italy
| | - Fabrizio Ceciliani
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
| | - Nuria Santos
- Department of Nutrition and Production of Herbivores, Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Sonia Andrés
- Department of Nutrition and Production of Herbivores, Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
- *Correspondence: Sonia Andrés,
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9
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Trivedi K, Kumar R, Vijay Anand KG, Bhojani G, Kubavat D, Ghosh A. Structural and functional changes in soil bacterial communities by drifting spray application of a commercial red seaweed extract as revealed by metagenomics. Arch Microbiol 2021; 204:72. [PMID: 34951686 DOI: 10.1007/s00203-021-02644-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 02/01/2023]
Abstract
Kappaphycus alvarezii seaweed extract (KSWE) is known to enhance crop productivity and impart stress tolerance. Close to one quarter of foliar spray applied to maize falls on the soil, either as drift or from leaf as drip. It was hypothesized that the drift spray would profoundly influence soil microbes under stress. An experiment was conducted with five treatments, with or without KSWE application at critical stages of maize grown under soil moisture stress and compared with an irrigated control. An Illumina platform was employed for the analysis of the V3-V4 region of 16S rRNA gene from the soil metagenome. A total of 345,552 operational taxonomic units were generated which were classified into 55 phyla, 152 classes, 240 orders, 305 families and 593 genera. Shannon's index and Shannon's equitability indicated increased soil bacterial diversity after multiple KSWE applications under conditions of abiotic duress. The abundance of the genera Alicyclobacillus, Anaerolinea, Bacillus, Balneimonas, Nitrospira, Rubrobacter and Steroidobacter decreased (49-79%) under drought imposed at the V5,10 and 15 stages of maize over the irrigated control, while it significantly improved when followed by KSWE application under drought. Flavobacterium, Nitrosomonas, Nitrosovibrio, Rubrobacter genera and several other bacterial taxa which are important for plant growth promotion and nutrient cycling were found to be enriched by KSWE application under drought conditions. Treatments having enriched microbial abundance due to KSWE application under stress recorded higher soil enzymatic activities and plant cob yield, suggesting the contribution of altered soil ecology mediated by KSWE as one of the reasons for improvement of yield.
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Affiliation(s)
- Khanjan Trivedi
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
| | - Ranjeet Kumar
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - K G Vijay Anand
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
| | - Gopal Bhojani
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Denish Kubavat
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arup Ghosh
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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10
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Latham LE, Wang C, Patterson TA, Slikker W, Liu F. Neuroprotective Effects of Carnitine and Its Potential Application to Ameliorate Neurotoxicity. Chem Res Toxicol 2021; 34:1208-1222. [PMID: 33570912 DOI: 10.1021/acs.chemrestox.0c00479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Carnitine is an essential metabolite that is absorbed from the diet and synthesized in the kidney, liver, and brain. It ferries fatty acids across the mitochondrial membrane to undergo β-oxidation. Carnitine has been studied as a therapy or protective agent for many neurological diseases and neurotoxicity (e.g., prolonged anesthetic exposure-induced developmental neurotoxicity in preclinical models). Preclinical and clinical data support the notion that carnitine or acetyl carnitine may improve a patient's quality of life through increased mitochondrial respiration, release of neurotransmitters, and global gene expression changes, showing the potential of carnitine beyond its approved use to treat primary and secondary carnitine deficiency. In this review, we summarize the beneficial effects of carnitine or acetyl carnitine on the central nervous system, highlighting protective effects against neurotoxicity-induced damage caused by various chemicals and encouraging a thorough evaluation of carnitine use as a therapy for patients suffering from neurotoxicant exposure.
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Affiliation(s)
- Leah E Latham
- Division of Neurotoxicology, National Center for Toxicological Research/FDA, Jefferson, Arkansas 72079, United States
| | - Cheng Wang
- Division of Neurotoxicology, National Center for Toxicological Research/FDA, Jefferson, Arkansas 72079, United States
| | - Tucker A Patterson
- Office of Director, National Center for Toxicological Research/FDA, Jefferson, Arkansas 72079, United States
| | - William Slikker
- Office of Director, National Center for Toxicological Research/FDA, Jefferson, Arkansas 72079, United States
| | - Fang Liu
- Division of Neurotoxicology, National Center for Toxicological Research/FDA, Jefferson, Arkansas 72079, United States
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11
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Increased Trimethylamine N-Oxide Is Not Associated with Oxidative Stress Markers in Healthy Aged Women. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:6247169. [PMID: 31636806 PMCID: PMC6766136 DOI: 10.1155/2019/6247169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/02/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
Abstract
Increased plasma trimethylamine N-oxide (TMAO) levels have been associated with cardiovascular diseases (CVD). L-carnitine induces TMAO elevation in human blood, and thus, it has been suggested as developing atherosclerosis. The aim of this study was to determine the relation between selected markers of oxidative stress and plasma TMAO concentration induced by L-carnitine supplementation for 24 weeks in healthy aged women. Twenty aged women were supplemented during 24 weeks with either 1500 mg L-carnitine-L-tartrate (n = 11) or isonitrogenous placebo (n = 9) per day. Fasting blood samples were taken from antecubital vein. L-carnitine supplementation induced an increase in TMAO, but not in γ-butyrobetaine (GBB). Moreover, there were no significant changes in serum ox-LDL, myeloperoxidase, protein carbonyls, homocysteine, and uric acid concentrations due to supplementation. Significant reduction in white blood cell counts has been observed following 24-week supplementation, but not attributable to L-carnitine. Our results in healthy aged women indicated no relation between TMAO and any determined marker of oxidative stress over the period of 24 weeks. At the same time, plasma GBB levels were not affected by L-carnitine supplementation. Further clinical studies of plasma GBB level as a prognostic marker are needed.
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12
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Breisch J, Waclawska I, Averhoff B. Identification and characterization of a carnitine transporter in Acinetobacter baumannii. Microbiologyopen 2019; 8:e00752. [PMID: 30318737 PMCID: PMC6562126 DOI: 10.1002/mbo3.752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 02/01/2023] Open
Abstract
The opportunistic pathogen Acinetobacter baumannii is able to grow on carnitine. The genes encoding the pathway for carnitine degradation to the intermediate malic acid are known but the transporter mediating carnitine uptake remained to be identified. The open reading frame HMPREF0010_01347 (aci01347) of Acinetobacter baumannii is annotated as a gene encoding a potential transporter of the betaine/choline/carnitine transporter (BCCT) family. To study the physiological function of Aci01347, the gene was deleted from A. baumannii ATCC 19606. The mutant was no longer able to grow on carnitine as sole carbon and energy source demonstrating the importance of this transporter for carnitine metabolism. Aci01347 was produced in Escherichia coli MKH13, a strain devoid of any compatible solute transporter, and the recombinant E. coli MKH13 strain was found to take up carnitine in an energy-dependent fashion. Aci01347 also transported choline, a compound known to be accumulated under osmotic stress. Choline transport was osmolarity-independent which is consistent with the absence of an extended C-terminus found in osmo-activated BCCT. We propose that the Aci01347 is the carnitine transporter mediating the first step in the growth of A. baumannii on carnitine.
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Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesGoethe‐University Frankfurt am MainFrankfurtGermany
| | - Izabela Waclawska
- Institute of Biophysics & Biophysical ChemistryUniversity RegensburgRegensburgGermany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesGoethe‐University Frankfurt am MainFrankfurtGermany
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13
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Characterization of l-Carnitine Metabolism in Sinorhizobium meliloti. J Bacteriol 2019; 201:JB.00772-18. [PMID: 30670548 DOI: 10.1128/jb.00772-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
l-Carnitine is a trimethylammonium compound mostly known for its contribution to fatty acid transport into mitochondria. In bacteria, it is synthesized from γ-butyrobetaine (GBB) and can be used as a carbon source. l-Carnitine can be formed directly by GBB hydroxylation or synthesized via a biosynthetic route analogous to fatty acid degradation. However, this multistep pathway has not been experimentally characterized. In this work, we identified by gene context analysis a cluster of l-carnitine anabolic genes next to those involved in its catabolism and proceeded to the complete in vitro characterization of l-carnitine biosynthesis and degradation in Sinorhizobium meliloti The five enzymes catalyzing the seven steps that convert GBB to glycine betaine are described. Metabolomic analysis confirmed the multistage synthesis of l-carnitine in GBB-grown cells but also revealed that GBB is synthesized by S. meliloti To our knowledge, this is the first report of aerobic GBB synthesis in bacteria. The conservation of l-carnitine metabolism genes in different bacterial taxonomic classes underscores the role of l-carnitine as a ubiquitous nutrient.IMPORTANCE The experimental characterization of novel metabolic pathways is essential for realizing the value of genome sequences and improving our knowledge of the enzymatic capabilities of the bacterial world. However, 30% to 40% of genes of a typical genome remain unannotated or associated with a putative function. We used enzyme kinetics, liquid chromatography-mass spectroscopy (LC-MS)-based metabolomics, and mutant phenotyping for the characterization of the metabolism of l-carnitine in Sinorhizobium meliloti to provide an accurate annotation of the corresponding genes. The occurrence of conserved gene clusters for carnitine metabolism in soil, plant-associated, and marine bacteria underlines the environmental abundance of carnitine and suggests this molecule might make a significant contribution to ecosystem nitrogen and carbon cycling.
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14
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Epigenetic findings in periodontitis in UK twins: a cross-sectional study. Clin Epigenetics 2019; 11:27. [PMID: 30760334 PMCID: PMC6375219 DOI: 10.1186/s13148-019-0614-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/11/2019] [Indexed: 02/08/2023] Open
Abstract
Background Genetic and environmental risk factors contribute to periodontal disease, but the underlying susceptibility pathways are not fully understood. Epigenetic mechanisms are malleable regulators of gene function that can change in response to genetic and environmental stimuli, thereby providing a potential mechanism for mediating risk effects in periodontitis. The aim of this study is to identify epigenetic changes across tissues that are associated with periodontal disease. Methods Self-reported gingival bleeding and history of gum disease, or tooth mobility, were used as indicators of periodontal disease. DNA methylation profiles were generated using the Infinium HumanMethylation450 BeadChip in whole blood, buccal, and adipose tissue samples from predominantly older female twins (mean age 58) from the TwinsUK cohort. Epigenome-wide association scans (EWAS) of gingival bleeding and tooth mobility were conducted in whole blood in 528 and 492 twins, respectively. Subsequently, targeted candidate gene analysis at 28 genomic regions was carried out testing for phenotype-methylation associations in 41 (tooth mobility) and 43 (gingival bleeding) buccal, and 501 (tooth mobility) and 556 (gingival bleeding) adipose DNA samples. Results Epigenome-wide analyses in blood identified one CpG-site (cg21245277 in ZNF804A) associated with gingival bleeding (FDR = 0.03, nominal p value = 7.17e−8) and 58 sites associated with tooth mobility (FDR < 0.05) with the top signals in IQCE and XKR6. Epigenetic variation at 28 candidate regions (247 CpG-sites) for chronic periodontitis showed an enrichment for association with periodontal traits, and signals in eight genes (VDR, IL6ST, TMCO6, IL1RN, CD44, IL1B, WHAMM, and CXCL1) were significant in both traits. The methylation-phenotype association signals validated in buccal samples, and a subset (25%) also validated in adipose tissue. Conclusions Epigenome-wide analyses in adult female twins identified specific DNA methylation changes linked to self-reported periodontal disease. Future work will explore the environmental basis and functional impact of these results to infer potential for strategic personalized treatments and prevention of chronic periodontitis. Electronic supplementary material The online version of this article (10.1186/s13148-019-0614-4) contains supplementary material, which is available to authorized users.
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15
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Koeth RA, Lam-Galvez BR, Kirsop J, Wang Z, Levison BS, Gu X, Copeland MF, Bartlett D, Cody DB, Dai HJ, Culley MK, Li XS, Fu X, Wu Y, Li L, DiDonato JA, Tang WHW, Garcia-Garcia JC, Hazen SL. l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans. J Clin Invest 2018; 129:373-387. [PMID: 30530985 DOI: 10.1172/jci94601] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND l-Carnitine, an abundant nutrient in red meat, accelerates atherosclerosis in mice via gut microbiota-dependent formation of trimethylamine (TMA) and trimethylamine N-oxide (TMAO) via a multistep pathway involving an atherogenic intermediate, γ-butyrobetaine (γBB). The contribution of γBB in gut microbiota-dependent l-carnitine metabolism in humans is unknown. METHODS Omnivores and vegans/vegetarians ingested deuterium-labeled l-carnitine (d3-l-carnitine) or γBB (d9-γBB), and both plasma metabolites and fecal polymicrobial transformations were examined at baseline, following oral antibiotics, or following chronic (≥2 months) l-carnitine supplementation. Human fecal commensals capable of performing each step of the l-carnitine→γBB→TMA transformation were identified. RESULTS Studies with oral d3-l-carnitine or d9-γBB before versus after antibiotic exposure revealed gut microbiota contribution to the initial 2 steps in a metaorganismal l-carnitine→γBB→TMA→TMAO pathway in subjects. Moreover, a striking increase in d3-TMAO generation was observed in omnivores over vegans/vegetarians (>20-fold; P = 0.001) following oral d3-l-carnitine ingestion, whereas fasting endogenous plasma l-carnitine and γBB levels were similar in vegans/vegetarians (n = 32) versus omnivores (n = 40). Fecal metabolic transformation studies, and oral isotope tracer studies before versus after chronic l-carnitine supplementation, revealed that omnivores and vegans/vegetarians alike rapidly converted carnitine to γBB, whereas the second gut microbial transformation, γBB→TMA, was diet inducible (l-carnitine, omnivorous). Extensive anaerobic subculturing of human feces identified no single commensal capable of l-carnitine→TMA transformation, multiple community members that converted l-carnitine to γBB, and only 1 Clostridiales bacterium, Emergencia timonensis, that converted γBB to TMA. In coculture, E. timonensis promoted the complete l-carnitine→TMA transformation. CONCLUSION In humans, dietary l-carnitine is converted into the atherosclerosis- and thrombosis-promoting metabolite TMAO via 2 sequential gut microbiota-dependent transformations: (a) initial rapid generation of the atherogenic intermediate γBB, followed by (b) transformation into TMA via low-abundance microbiota in omnivores, and to a markedly lower extent, in vegans/vegetarians. Gut microbiota γBB→TMA/TMAO transformation is induced by omnivorous dietary patterns and chronic l-carnitine exposure. TRIAL REGISTRATION ClinicalTrials.gov NCT01731236. FUNDING NIH and Office of Dietary Supplements grants HL103866, HL126827, and DK106000, and the Leducq Foundation.
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Affiliation(s)
- Robert A Koeth
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Jennifer Kirsop
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Zeneng Wang
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Bruce S Levison
- Department of Cellular and Molecular Medicine, Lerner Research Institute
| | - Xiaodong Gu
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | | | - David Bartlett
- Department of Cellular and Molecular Medicine, Lerner Research Institute
| | | | - Hong J Dai
- Global Biosciences, The Procter & Gamble Company, Cincinnati, Ohio, USA
| | - Miranda K Culley
- Department of Cellular and Molecular Medicine, Lerner Research Institute
| | - Xinmin S Li
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Xiaoming Fu
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Yuping Wu
- Department of Mathematics, Cleveland State University, Cleveland, Ohio, USA
| | - Lin Li
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Joseph A DiDonato
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - W H Wilson Tang
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
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16
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van der Hoek MD, Madsen O, Keijer J, van der Leij FR. Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of CPT2 versus CPT1 and related variants. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:909-918. [PMID: 29730527 DOI: 10.1016/j.bbalip.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 10/17/2022]
Abstract
Carnitine/choline acyltransferases play diverse roles in energy metabolism and neuronal signalling. Our knowledge of their evolutionary relationships, important for functional understanding, is incomplete. Therefore, we aimed to determine the evolutionary relationships of these eukaryotic transferases. We performed extensive phylogenetic and intron position analyses. We found that mammalian intramitochondrial CPT2 is most closely related to cytosolic yeast carnitine transferases (Sc-YAT1 and 2), whereas the other members of the family are related to intraorganellar yeast Sc-CAT2. Therefore, the cytosolically active CPT1 more closely resembles intramitochondrial ancestors than CPT2. The choline acetyltransferase is closely related to carnitine acetyltransferase and shows lower evolutionary rates than long chain acyltransferases. In the CPT1 family several duplications occurred during animal radiation, leading to the isoforms CPT1A, CPT1B and CPT1C. In addition, we found five CPT1-like genes in Caenorhabditis elegans that strongly group to the CPT1 family. The long branch leading to mammalian brain isoform CPT1C suggests that either strong positive or relaxed evolution has taken place on this node. The presented evolutionary delineation of carnitine/choline acyltransferases adds to current knowledge on their functions and provides tangible leads for further experimental research.
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Affiliation(s)
- Marjanne D van der Hoek
- Applied Research Centre Food and Dairy, Van Hall Larenstein University of Applied Sciences, P.O. box 1528, 8901BV Leeuwarden, The Netherlands; Human and Animal Physiology, Wageningen University, P.O. box 338, 6700AH Wageningen, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics Centre, Wageningen University, P.O. box 338, 6700AH Wageningen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, P.O. box 338, 6700AH Wageningen, The Netherlands
| | - Feike R van der Leij
- Applied Research Centre Food and Dairy, Van Hall Larenstein University of Applied Sciences, P.O. box 1528, 8901BV Leeuwarden, The Netherlands.
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17
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Ghonimy A, Zhang DM, Farouk MH, Wang Q. The Impact of Carnitine on Dietary Fiber and Gut Bacteria Metabolism and Their Mutual Interaction in Monogastrics. Int J Mol Sci 2018; 19:E1008. [PMID: 29597260 PMCID: PMC5979481 DOI: 10.3390/ijms19041008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/06/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Carnitine has vital roles in the endogenous metabolism of short chain fatty acids. It can protect and support gut microbial species, and some dietary fibers can reduce the available iron involved in the bioactivity of carnitine. There is also an antagonistic relationship between high microbial populations and carnitine bioavailability. This review shows the interactions between carnitine and gut microbial composition. It also elucidates the role of carnitine bacterial metabolism, mitochondrial function, fiber fermentability, and short chain fatty acids (SCFAs).
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Affiliation(s)
- Abdallah Ghonimy
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Dong Ming Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
- Tonghua Normal University, Tonghua 134000, China.
| | - Mohammed Hamdy Farouk
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
- Department of Animal Production, Faculty of Agriculture, Al-Azhar University, Cairo 11884, Egypt.
| | - Qiuju Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
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18
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Metabolomics studies on db/db diabetic mice in skeletal muscle reveal effective clearance of overloaded intermediates by exercise. Anal Chim Acta 2017; 1037:130-139. [PMID: 30292287 DOI: 10.1016/j.aca.2017.11.082] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 12/17/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by hyperinsulinemia, hyperglycemia and insulin resistance, which correlated with high mortality worldwide. Exercise is one of the effective lifestyle interventions in maintaining blood glucose level in the normal range and lowering risk factors. Metabolomics approaches are powerful tools in systematic study of overall metabolic changes in response to disease or interventions. In this study, mass spectrometry-based metabolomics studies were performed to investigate the regulatory effect of moderate intensity of exercise on db/db diabetic mice in skeletal muscle. Both liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) have been carried out to monitor a wide range of regulated metabolites. Ninety-five metabolites were identified which contributing to the discrimination of db/m + control and db/db diabetic mice. The regulatory effects of exercise on these metabolites were mainly focusing on attenuating the levels of long-chain fatty acids (C14 to C18) and medium-to long-chain acylcarnitines (C12 to C18), indicated that exercise might play a positive role in inhibiting the accumulation of excessive lipids, which is positively related to insulin resistance. In addition, uric acid, which is a risk factor for inflammation, cardiovascular complications, and fatty liver in diabetic patients, together with its intermediates (such as inosinic acid, hypoxanthine, etc.) in purine metabolism pathway, were also substantially down regulated after exercise, indicating exercise might also be protective against hyperuricemia related risks in T2DM. These findings reveal that moderate intensity of exercise might play a positive role in improving the efficiency of lipid metabolism in skeletal muscle and meanwhile enhancing uric acid clearance to prevent lipid accumulation, which might contribute to improved body fitness and body muscle composition.
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19
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Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. THE ISME JOURNAL 2017; 11:1483-1499. [PMID: 28106881 PMCID: PMC5437341 DOI: 10.1038/ismej.2016.198] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/29/2016] [Accepted: 11/19/2016] [Indexed: 12/31/2022]
Abstract
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.
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Affiliation(s)
- Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Helmholtz Centre for Infection Research, Research Group Microbial Communication, Braunschweig, Germany
| | - Marcus Ulbrich
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Dietmar Schomburg
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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20
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Shea AA, Bernhards RC, Cote CK, Chase CJ, Koehler JW, Klimko CP, Ladner JT, Rozak DA, Wolcott MJ, Fetterer DP, Kern SJ, Koroleva GI, Lovett SP, Palacios GF, Toothman RG, Bozue JA, Worsham PL, Welkos SL. Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences. PLoS One 2017; 12:e0171363. [PMID: 28187198 PMCID: PMC5302386 DOI: 10.1371/journal.pone.0171363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/18/2017] [Indexed: 12/12/2022] Open
Abstract
Burkholderia pseudomallei (Bp), the agent of melioidosis, causes disease ranging from acute and rapidly fatal to protracted and chronic. Bp is highly infectious by aerosol, can cause severe disease with nonspecific symptoms, and is naturally resistant to multiple antibiotics. However, no vaccine exists. Unlike many Bp strains, which exhibit random variability in traits such as colony morphology, Bp strain MSHR5848 exhibited two distinct and relatively stable colony morphologies on sheep blood agar plates: a smooth, glossy, pale yellow colony and a flat, rough, white colony. Passage of the two variants, designated "Smooth" and "Rough", under standard laboratory conditions produced cultures composed of > 99.9% of the single corresponding type; however, both could switch to the other type at different frequencies when incubated in certain nutritionally stringent or stressful growth conditions. These MSHR5848 derivatives were extensively characterized to identify variant-associated differences. Microscopic and colony morphology differences on six differential media were observed and only the Rough variant metabolized sugars in selective agar. Antimicrobial susceptibilities and lipopolysaccharide (LPS) features were characterized and phenotype microarray profiles revealed distinct metabolic and susceptibility disparities between the variants. Results using the phenotype microarray system narrowed the 1,920 substrates to a subset which differentiated the two variants. Smooth grew more rapidly in vitro than Rough, yet the latter exhibited a nearly 10-fold lower lethal dose for mice than Smooth. Finally, the Smooth variant was phagocytosed and replicated to a greater extent and was more cytotoxic than Rough in macrophages. In contrast, multiple locus sequence type (MLST) analysis, ribotyping, and whole genome sequence analysis demonstrated the variants' genetic conservation; only a single consistent genetic difference between the two was identified for further study. These distinct differences shown by two variants of a Bp strain will be leveraged to better understand the mechanism of Bp phenotypic variability and to possibly identify in vitro markers of infection.
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Affiliation(s)
- A. A. Shea
- Diagnostic Systems Division, USAMRIID, Frederick, Maryland, United States of America
| | - R. C. Bernhards
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
| | - C. K. Cote
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
| | - C. J. Chase
- Diagnostic Systems Division, USAMRIID, Frederick, Maryland, United States of America
| | - J. W. Koehler
- Diagnostic Systems Division, USAMRIID, Frederick, Maryland, United States of America
| | - C. P. Klimko
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
| | - J. T. Ladner
- Center for Genome Sciences, USAMRIID, Frederick, Maryland, United States of America
| | - D. A. Rozak
- Diagnostic Systems Division, USAMRIID, Frederick, Maryland, United States of America
| | - M. J. Wolcott
- Diagnostic Systems Division, USAMRIID, Frederick, Maryland, United States of America
| | - D. P. Fetterer
- Biostatistical Services Division, USAMRIID, Frederick, Maryland, United States of America
| | - S. J. Kern
- Biostatistical Services Division, USAMRIID, Frederick, Maryland, United States of America
| | - G. I. Koroleva
- Center for Genome Sciences, USAMRIID, Frederick, Maryland, United States of America
| | - S. P. Lovett
- Center for Genome Sciences, USAMRIID, Frederick, Maryland, United States of America
| | - G. F. Palacios
- Center for Genome Sciences, USAMRIID, Frederick, Maryland, United States of America
| | - R. G. Toothman
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
| | - J. A. Bozue
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
| | - P. L. Worsham
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
| | - S. L. Welkos
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland, United States of America
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Mohamed Ahmed IA, Eltayeb MM, Habora ME, Eltayeb AE, Arima J, Mori N, Taniguchi T, Yamanaka N. Identification of the key genes involved in the degradation of homocholine by Pseudomonas sp. strain A9 by using suppression subtractive hybridization. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Molina-Quiroz RC, Silva CA, Molina CF, Leiva LE, Reyes-Cerpa S, Contreras I, Santiviago CA. Exposure to sub-inhibitory concentrations of cefotaxime enhances the systemic colonization of Salmonella Typhimurium in BALB/c mice. Open Biol 2016; 5:rsob.150070. [PMID: 26468132 PMCID: PMC4632510 DOI: 10.1098/rsob.150070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It has been proposed that sub-inhibitory concentrations of antibiotics play a role in virulence modulation. In this study, we evaluated the ability of Salmonella enterica serovar Typhimurium (hereafter S. Typhimurium) to colonize systemically BALB/c mice after exposure to a sub-inhibitory concentration of cefotaxime (CTX). In vivo competition assays showed a fivefold increase in systemic colonization of CTX-exposed bacteria when compared to untreated bacteria. To identify the molecular mechanisms involved in this phenomenon, we carried out a high-throughput genetic screen. A transposon library of S. Typhimurium mutants was subjected to negative selection in the presence of a sub-inhibitory concentration of CTX and genes related to anaerobic metabolism, biosynthesis of purines, pyrimidines, amino acids and other metabolites were identified as needed to survive in this condition. In addition, an impaired ability for oxygen consumption was observed when bacteria were cultured in the presence of a sub-inhibitory concentration of CTX. Altogether, our data indicate that exposure to sub-lethal concentrations of CTX increases the systemic colonization of S. Typhimurium in BALB/c mice in part by the establishment of a fitness alteration conducive to anaerobic metabolism.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile Center for Adaptation Genetics and Drugs Resistance, Molecular Biology and Microbiology Faculty, Tufts University, Boston, MA, USA
| | - Cecilia A Silva
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | - Lorenzo E Leiva
- Centro de InmunoBioTecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Sebastián Reyes-Cerpa
- Laboratorio de Virología, Centro de Biotecnología Acuícola (CBA), Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Inés Contreras
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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23
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Fennema D, Phillips IR, Shephard EA. Trimethylamine and Trimethylamine N-Oxide, a Flavin-Containing Monooxygenase 3 (FMO3)-Mediated Host-Microbiome Metabolic Axis Implicated in Health and Disease. ACTA ACUST UNITED AC 2016; 44:1839-1850. [PMID: 27190056 PMCID: PMC5074467 DOI: 10.1124/dmd.116.070615] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/13/2016] [Indexed: 02/06/2023]
Abstract
Flavin-containing monooxygenase 3 (FMO3) is known primarily as an enzyme involved in the metabolism of therapeutic drugs. On a daily basis, however, we are exposed to one of the most abundant substrates of the enzyme trimethylamine (TMA), which is released from various dietary components by the action of gut bacteria. FMO3 converts the odorous TMA to nonodorous TMA N-oxide (TMAO), which is excreted in urine. Impaired FMO3 activity gives rise to the inherited disorder primary trimethylaminuria (TMAU). Affected individuals cannot produce TMAO and, consequently, excrete large amounts of TMA. A dysbiosis in gut bacteria can give rise to secondary TMAU. Recently, there has been much interest in FMO3 and its catalytic product, TMAO, because TMAO has been implicated in various conditions affecting health, including cardiovascular disease, reverse cholesterol transport, and glucose and lipid homeostasis. In this review, we consider the dietary components that can give rise to TMA, the gut bacteria involved in the production of TMA from dietary precursors, the metabolic reactions by which bacteria produce and use TMA, and the enzymes that catalyze the reactions. Also included is information on bacteria that produce TMA in the oral cavity and vagina, two key microbiome niches that can influence health. Finally, we discuss the importance of the TMA/TMAO microbiome-host axis in health and disease, considering factors that affect bacterial production and host metabolism of TMA, the involvement of TMAO and FMO3 in disease, and the implications of the host-microbiome axis for management of TMAU.
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Affiliation(s)
- Diede Fennema
- Institute of Structural and Molecular Biology, University College London (D.F., I.R.P., E.A.S.), and School of Biological and Chemical Sciences, Queen Mary University of London (I.R.P.), London, United Kingdom
| | - Ian R Phillips
- Institute of Structural and Molecular Biology, University College London (D.F., I.R.P., E.A.S.), and School of Biological and Chemical Sciences, Queen Mary University of London (I.R.P.), London, United Kingdom
| | - Elizabeth A Shephard
- Institute of Structural and Molecular Biology, University College London (D.F., I.R.P., E.A.S.), and School of Biological and Chemical Sciences, Queen Mary University of London (I.R.P.), London, United Kingdom
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24
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Kamps JJAG, Khan A, Choi H, Lesniak RK, Brem J, Rydzik AM, McDonough MA, Schofield CJ, Claridge TDW, Mecinović J. Cation-π Interactions Contribute to Substrate Recognition in γ-Butyrobetaine Hydroxylase Catalysis. Chemistry 2015; 22:1270-6. [PMID: 26660433 PMCID: PMC4736438 DOI: 10.1002/chem.201503761] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Indexed: 11/08/2022]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a non-heme Fe(II) - and 2-oxoglutarate-dependent oxygenase that catalyzes the stereoselective hydroxylation of an unactivated C-H bond of γ-butyrobetaine (γBB) in the final step of carnitine biosynthesis. BBOX contains an aromatic cage for the recognition of the positively charged trimethylammonium group of the γBB substrate. Enzyme binding and kinetic analyses on substrate analogues with P and As substituting for N in the trimethylammonium group show that the analogues are good BBOX substrates, which follow the efficiency trend N(+) >P(+) >As(+). The results reveal that an uncharged carbon analogue of γBB is not a BBOX substrate, thus highlighting the importance of the energetically favorable cation-π interactions in productive substrate recognition.
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Affiliation(s)
- Jos J A G Kamps
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Amjad Khan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Robert K Lesniak
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Anna M Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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Rydzik AM, Leung IKH, Kochan GT, Loik ND, Henry L, McDonough MA, Claridge TDW, Schofield CJ. Comparison of the substrate selectivity and biochemical properties of human and bacterial γ-butyrobetaine hydroxylase. Org Biomol Chem 2015; 12:6354-8. [PMID: 25030770 DOI: 10.1039/c4ob01167h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
2-Oxoglutarate and iron dependent oxygenases have potential for the stereoselective hydroxylation of amino acids and related compounds. The biochemical and kinetic properties of recombinant γ-butyrobetaine hydroxylase from human and Pseudomonas sp. AK1 were compared. The results reveal differences between the two BBOXs, including in their stimulation by ascorbate. Despite their closely related sequences, the two enzymes also display different substrate selectivities, including for the production of (di)hydroxylated betaines, implying use of engineered BBOXs for biocatalytic purposes may be productive.
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Affiliation(s)
- Anna M Rydzik
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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Meadows JA, Wargo MJ. Carnitine in bacterial physiology and metabolism. MICROBIOLOGY (READING, ENGLAND) 2015; 161:1161-74. [PMID: 25787873 PMCID: PMC4635513 DOI: 10.1099/mic.0.000080] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/17/2015] [Indexed: 12/23/2022]
Abstract
Carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. In bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. Carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized through one of a few distinct pathways as a nutrient source. In this review, we summarize what is known about carnitine physiology and metabolism in bacteria. In particular, recent advances in the aerobic and anaerobic metabolic pathways as well as the use of carnitine as an electron acceptor have addressed some long-standing questions in the field.
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Affiliation(s)
- Jamie A. Meadows
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, 95 Carrigan Drive, Burlington, VT, 05405, USA
| | - Matthew J. Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, 95 Carrigan Drive, Burlington, VT, 05405, USA
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Vaz FM, van Vlies N. Dioxygenases of Carnitine Biosynthesis: 6- N-Trimethyllysine and γ-Butyrobetaine Hydroxylases. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter describes the state of knowledge of the two 2-oxoglutarate-dependent dioxygenases of carnitine biosynthesis: 6-N-trimethyllysine hydroxylase and γ-butyrobetaine hydroxylase. Both enzymes have been extensively investigated as carnitine plays an important role in fatty acid metabolism in animals and some other life forms. Carnitine metabolism is introduced followed by a comprehensive review of the properties of the two carnitine biosynthesis dioxygenases including their purification, kinetic and biophysical characterization, regulation and roles in metabolism.
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Affiliation(s)
- Frédéric M. Vaz
- Laboratory Genetic Metabolic Diseases, Departments of Paediatrics and Clinical Chemistry, Emma Children’s Hospital, Academic Medical Center 1105 AZ Amsterdam The Netherlands
| | - Naomi van Vlies
- Laboratory Genetic Metabolic Diseases, Departments of Paediatrics and Clinical Chemistry, Emma Children’s Hospital, Academic Medical Center 1105 AZ Amsterdam The Netherlands
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29
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Koeth RA, Levison BS, Culley MK, Buffa JA, Wang Z, Gregory JC, Org E, Wu Y, Li L, Smith JD, Tang WHW, DiDonato JA, Lusis AJ, Hazen SL. γ-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO. Cell Metab 2014; 20:799-812. [PMID: 25440057 PMCID: PMC4255476 DOI: 10.1016/j.cmet.2014.10.006] [Citation(s) in RCA: 384] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/05/2014] [Accepted: 10/13/2014] [Indexed: 01/30/2023]
Abstract
L-carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein, we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ∼1,000-fold higher than the formation of TMA. Moreover, we show that γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, is converted into TMA and TMAO in a gut microbiota-dependent manner (like dietary L-carnitine), and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal that distinct taxa are associated with the production of γBB or TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine or γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine or γBB, respectively.
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Affiliation(s)
- Robert A Koeth
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bruce S Levison
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Miranda K Culley
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jennifer A Buffa
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jill C Gregory
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Elin Org
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Yuping Wu
- Department of Mathematics, Cleveland State University, Cleveland, OH 44115, USA
| | - Lin Li
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jonathan D Smith
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - W H Wilson Tang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Joseph A DiDonato
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Aldons J Lusis
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Stanley L Hazen
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.
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Kuka J, Liepinsh E, Makrecka-Kuka M, Liepins J, Cirule H, Gustina D, Loza E, Zharkova-Malkova O, Grinberga S, Pugovics O, Dambrova M. Suppression of intestinal microbiota-dependent production of pro-atherogenic trimethylamine N-oxide by shifting L-carnitine microbial degradation. Life Sci 2014; 117:84-92. [PMID: 25301199 DOI: 10.1016/j.lfs.2014.09.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/28/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
Abstract
AIMS Trimethylamine-N-oxide (TMAO) is produced in host liver from trimethylamine (TMA). TMAO and TMA share common dietary quaternary amine precursors, carnitine and choline, which are metabolized by the intestinal microbiota. TMAO recently has been linked to the pathogenesis of atherosclerosis and severity of cardiovascular diseases. We examined the effects of anti-atherosclerotic compound meldonium, an aza-analogue of carnitine bioprecursor gamma-butyrobetaine (GBB), on the availability of TMA and TMAO. MAIN METHODS Wistar rats received L-carnitine, GBB or choline alone or in combination with meldonium. Plasma, urine and rat small intestine perfusate samples were assayed for L-carnitine, GBB, choline and TMAO using UPLC-MS/MS. Meldonium effects on TMA production by intestinal bacteria from L-carnitine and choline were tested. KEY FINDINGS Treatment with meldonium significantly decreased intestinal microbiota-dependent production of TMA/TMAO from L-carnitine, but not from choline. 24hours after the administration of meldonium, the urinary excretion of TMAO was 3.6 times lower in the combination group than in the L-carnitine-alone group. In addition, the administration of meldonium together with L-carnitine significantly increased GBB concentration in blood plasma and in isolated rat small intestine perfusate. Meldonium did not influence bacterial growth and bacterial uptake of L-carnitine, but TMA production by the intestinal microbiota bacteria K. pneumoniae was significantly decreased. SIGNIFICANCE We have shown for the first time that TMA/TMAO production from quaternary amines could be decreased by targeting bacterial TMA-production. In addition, the production of pro-atherogenic TMAO can be suppressed by shifting the microbial degradation pattern of supplemental/dietary quaternary amines.
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Affiliation(s)
- Janis Kuka
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia.
| | - Edgars Liepinsh
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia
| | - Marina Makrecka-Kuka
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia; Rigas Stradins University, Dzirciema Str. 16, Riga, LV-1007, Latvia
| | - Janis Liepins
- University of Latvia, Institute of Microbiology and Biotechnology, Kronvalda Blvd. 4, Riga LV-1586, Latvia
| | - Helena Cirule
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia
| | - Daina Gustina
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia
| | - Einars Loza
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia
| | | | - Solveiga Grinberga
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia
| | - Osvalds Pugovics
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia
| | - Maija Dambrova
- Latvian Institute of Organic Synthesis, Aizkraukles Str. 21, Riga, LV-1006, Latvia; Rigas Stradins University, Dzirciema Str. 16, Riga, LV-1007, Latvia
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Rashidi-Nezhad A, Talebi S, Saebnouri H, Akrami SM, Reymond A. The effect of homozygous deletion of the BBOX1 and Fibin genes on carnitine level and acyl carnitine profile. BMC MEDICAL GENETICS 2014; 15:75. [PMID: 24986124 PMCID: PMC4184381 DOI: 10.1186/1471-2350-15-75] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 06/26/2014] [Indexed: 11/10/2022]
Abstract
Background Carnitine is a key molecule in energy metabolism that helps transport activated fatty acids into the mitochondria. Its homeostasis is achieved through oral intake, renal reabsorption and de novo biosynthesis. Unlike dietary intake and renal reabsorption, the importance of de novo biosynthesis pathway in carnitine homeostasis remains unclear, due to lack of animal models and description of a single patient defective in this pathway. Case presentation We identified by array comparative genomic hybridization a 42 months-old girl homozygote for a 221 Kb interstitial deletions at 11p14.2, that overlaps the genes encoding Fibin and butyrobetaine-gamma 2-oxoglutarate dioxygenase 1 (BBOX1), an enzyme essential for the biosynthesis of carnitine de novo. She presented microcephaly, speech delay, growth retardation and minor facial anomalies. The levels of almost all evaluated metabolites were normal. Her serum level of free carnitine was at the lower limit of the reference range, while her acylcarnitine to free carnitine ratio was normal. Conclusions We present an individual with a completely defective carnitine de novo biosynthesis. This condition results in mildly decreased free carnitine level, but not in clinical manifestations characteristic of carnitine deficiency disorders, suggesting that dietary carnitine intake and renal reabsorption are sufficient to carnitine homeostasis. Our results also demonstrate that haploinsufficiency of BBOX1 and/or Fibin is not associated with Primrose syndrome as previously suggested.
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Affiliation(s)
| | | | | | - Seyed Mohammad Akrami
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
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Revealing the hidden functional diversity of an enzyme family. Nat Chem Biol 2013; 10:42-9. [DOI: 10.1038/nchembio.1387] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/02/2013] [Indexed: 11/08/2022]
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Arginine oscillation explains Na+ independence in the substrate/product antiporter CaiT. Proc Natl Acad Sci U S A 2013; 110:17296-301. [PMID: 24101465 DOI: 10.1073/pnas.1309071110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most secondary-active transporters transport their substrates using an electrochemical ion gradient. In contrast, the carnitine transporter (CaiT) is an ion-independent, l-carnitine/γ-butyrobetaine antiporter belonging to the betaine/carnitine/choline transporter family of secondary transporters. Recently determined crystal structures of CaiT from Escherichia coli and Proteus mirabilis revealed an inverted five-transmembrane-helix repeat similar to that in the amino acid/Na(+) symporter LeuT. The ion independence of CaiT makes it unique in this family. Here we show that mutations of arginine 262 (R262) make CaiT Na(+)-dependent. The transport activity of R262 mutants increased by 30-40% in the presence of a membrane potential, indicating substrate/Na(+) cotransport. Structural and biochemical characterization revealed that R262 plays a crucial role in substrate binding by stabilizing the partly unwound TM1' helix. Modeling CaiT from P. mirabilis in the outward-open and closed states on the corresponding structures of the related symporter BetP reveals alternating orientations of the buried R262 sidechain, which mimic sodium binding and unbinding in the Na(+)-coupled substrate symporters. We propose that a similar mechanism is operative in other Na(+)/H(+)-independent transporters, in which a positively charged amino acid replaces the cotransported cation. The oscillation of the R262 sidechain in CaiT indicates how a positive charge triggers the change between outward-open and inward-open conformations as a unifying critical step in LeuT-type transporters.
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Sharma AK, Becker JW, Ottesen EA, Bryant JA, Duhamel S, Karl DM, Cordero OX, Repeta DJ, DeLong EF. Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations ofProchlorococcus,Pelagibacterand the OM60 clade. Environ Microbiol 2013; 16:2815-30. [DOI: 10.1111/1462-2920.12254] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/26/2013] [Accepted: 08/15/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Adrian K. Sharma
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Jamie W. Becker
- Department of Marine Chemistry and Geochemistry; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Elizabeth A. Ottesen
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Department of Microbiology; University of Georgia; Athens GA 30602 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Jessica A. Bryant
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Solange Duhamel
- Department of Marine Chemistry and Geochemistry; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
- Lamont Doherty Earth Observatory; Columbia University; Palisades NY 10964 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - David M. Karl
- Department of Oceanography; School of Ocean and Earth Science and Technology (SOEST); University of Hawaii; Honolulu HI 96822 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Otto X. Cordero
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Edward F. DeLong
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
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Metabolomic analyses of faeces reveals malabsorption in cirrhotic patients. Dig Liver Dis 2013; 45:677-82. [PMID: 23384618 DOI: 10.1016/j.dld.2013.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/21/2012] [Accepted: 01/01/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND The study of faeces offers a unique opportunity to observe cooperation between the microbiome and the metabolism of mammalian hosts, an essential element in the study of the human metabolome. In the present study, a global metabolomics approach was used to identify metabolites differentially excreted in the faeces of cirrhotic patients compared to controls. METHODS Seventeen cirrhotic patients and 24 healthy individuals were recruited. Faecal metabolites were detected through non-targeted reversed-phase ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. RESULTS A total of 9215 peaks were detected. Using unequal variance t-tests, 2393 peaks were observed with P≤0.05, approximately 74.0% of which were due to decreased faecal metabolite concentrations in liver cirrhosis vs. healthy controls. Integrating multivariate data analyses, we identified six major groups of metabolites. Relative levels of identified metabolites were as follows: strong increase in lysophosphatidylcholines, aromatic amino acids, fatty acids, and acylcarnitines, and a dramatic decrease in bile acids and bile pigments. CONCLUSION With severe hepatic injury in patients with liver cirrhosis, malabsorption occurs along with disorders of fatty acid metabolism, potentially due to changes in gut microflora.
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Arense P, Bernal V, Charlier D, Iborra JL, Foulquié-Moreno MR, Cánovas M. Metabolic engineering for high yielding L(-)-carnitine production in Escherichia coli. Microb Cell Fact 2013; 12:56. [PMID: 23718679 PMCID: PMC3680233 DOI: 10.1186/1475-2859-12-56] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 05/07/2013] [Indexed: 12/02/2022] Open
Abstract
Background L(-)-carnitine production has been widely studied because of its beneficial properties on various diseases and dysfunctions. Enterobacteria possess a specific biotransformation pathway which can be used for the enantioselective production of L(-)-carnitine. Although bioprocesses catalyzed by enzymes or whole cells can overcome the lack of enantioselectivity of chemical methods, current processes for L(−)-carnitine production still have severe disadvantages, such as the low yields, side reactions and the need of high catalyst concentrations and anaerobic conditions for proper expression of the biotransformation pathway. Additionally, genetically engineered strains so far constructed for L(-)-carnitine production are based on plasmids and, therefore, suffer from segregational unstability. Results In this work, a stable, high yielding strain for L(-)-carnitine production from low cost substrates was constructed. A metabolic engineering strategy was implemented in a multiple mutant for use in both growing and resting cells systems. The effect of mutations on gene expression and metabolism was analyzed to characterize the productivity constraints of the wild type and the overproducer strains. Precise deletion of genes which encode proteins of central and carnitine metabolisms were performed. Specifically, flux through the TCA cycle was increased by deletion of aceK (which encodes a bifunctional kinase/phosphatase which inhibits isocitrate dehydrogenase activity) and the synthesis of the by-product γ-butyrobetaine was prevented by deletion of caiA (which encodes a crotonobetainyl-CoA reductase). Both mutations led to improve the L(-)-carnitine production by 20 and 42%, respectively. Moreover, the highly regulated promoter of the cai operon was substituted by a constitutive artificial promoter increasing the biotransformation rate, even under aerobic conditions. Resting cells of the BW ΔaceK ΔcaiA p37cai strain produced 59.6 mmol l-1 · h-1 of L(−)-carnitine, doubling the productivity of the wild type strain. In addition, almost total conversion was attained in less than two hours without concomitant production of the side product γ–butyrobetaine. Conclusions L(-)-carnitine production has been enhanced by strain engineering. Metabolic engineering strategies herein implemented allowed obtaining a robust and high yielding E. coli strain. The new overproducer strain attained almost complete conversion of crotonobetaine into L(-)-carnitine with growing and resting cells, and even under aerobic conditions, overcoming the main environmental restriction to carnitine metabolism expression. So far, this is the best performing L(-)-carnitine production E. coli strain described.
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Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WHW, Bushman FD, Lusis AJ, Hazen SL. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 2013; 19:576-85. [PMID: 23563705 PMCID: PMC3650111 DOI: 10.1038/nm.3145] [Citation(s) in RCA: 2930] [Impact Index Per Article: 266.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/27/2013] [Indexed: 02/07/2023]
Abstract
Intestinal microbiota metabolism of choline and phosphatidylcholine produces trimethylamine (TMA), which is further metabolized to a proatherogenic species, trimethylamine-N-oxide (TMAO). We demonstrate here that metabolism by intestinal microbiota of dietary L-carnitine, a trimethylamine abundant in red meat, also produces TMAO and accelerates atherosclerosis in mice. Omnivorous human subjects produced more TMAO than did vegans or vegetarians following ingestion of L-carnitine through a microbiota-dependent mechanism. The presence of specific bacterial taxa in human feces was associated with both plasma TMAO concentration and dietary status. Plasma L-carnitine levels in subjects undergoing cardiac evaluation (n = 2,595) predicted increased risks for both prevalent cardiovascular disease (CVD) and incident major adverse cardiac events (myocardial infarction, stroke or death), but only among subjects with concurrently high TMAO levels. Chronic dietary L-carnitine supplementation in mice altered cecal microbial composition, markedly enhanced synthesis of TMA and TMAO, and increased atherosclerosis, but this did not occur if intestinal microbiota was concurrently suppressed. In mice with an intact intestinal microbiota, dietary supplementation with TMAO or either carnitine or choline reduced in vivo reverse cholesterol transport. Intestinal microbiota may thus contribute to the well-established link between high levels of red meat consumption and CVD risk.
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Affiliation(s)
- Robert A. Koeth
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Zeneng Wang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Bruce S. Levison
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Jennifer A. Buffa
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Elin Org
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles 90095, USA
| | - Brendan T. Sheehy
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Earl B. Britt
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Xiaoming Fu
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Yuping Wu
- Department of Mathematics, Cleveland State University, Cleveland, Ohio 44115, USA
| | - Lin Li
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Jonathan D. Smith
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Joseph A. DiDonato
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Jun Chen
- Department of Microbiology, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongzhe Li
- Department of Microbiology, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gary D. Wu
- Division of Gastroenterology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James D. Lewis
- Department of Microbiology, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manya Warrier
- Department of Pathology, Section on Lipid Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - J. Mark Brown
- Department of Pathology, Section on Lipid Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Ronald M. Krauss
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - W. H. Wilson Tang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Frederic D. Bushman
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Aldons J. Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles 90095, USA
| | - Stanley L. Hazen
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
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Gene cloning and biochemical characterization of 4-N-trimethylaminobutyraldehyde dehydrogenase II from Pseudomonas sp. 13CM. World J Microbiol Biotechnol 2012; 29:683-92. [PMID: 23225139 DOI: 10.1007/s11274-012-1224-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
The gene encoding 4-N-trimethylaminobutyraldehyde dehydrogenase (TMABaldehyde-DH) from Pseudomonas sp. 13CM, responsible for the conversion of 4-N-trimethylaminobutyraldehyde (TMABaldehyde) to γ-butyrobetaine in the carnitine biosynthesis pathway, isolated by shotgun cloning and expressed in Escherichia coli DH5α. The recombinant TMABaldehyde-DH was purified 19.5 fold to apparent homogeneity by hydrophobic and affinity chromatography and biochemically characterized. The enzyme was found to be a trimer with identical 52 kDa subunits. The isoelectric point was found to be 4.5. Optimum pH and temperature were found respectively as pH 9.5 and 40 °C. The Km values for TMABaldehyde, 4-dimethylaminobutyraldehyde, and NAD+ were respectively, 0.31, 0.62, and 1.16 mM. The molecular and catalytic properties differed from those of TMABaldehyde-DH I, which was discovered initially in Pseudomonas sp. 13CM. The new enzyme, designated TMABaldehyde-DH II, structural gene was inserted into an expression vector pET24b (+) and over-expressed in E. coli BL21 (DE3) under the control of a T7 promoter. The recombinant TMABaldehyde-DH from Pseudomonas sp. 13CM can now be obtained in large quantity necessary for further biochemical characterization and applications.
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Zomot E, Bahar I. A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ-butyrobetaine antiporter CaiT. J Biol Chem 2012; 287:31823-32. [PMID: 22843728 PMCID: PMC3442516 DOI: 10.1074/jbc.m112.397364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CaiT is a homotrimeric antiporter that exchanges l-carnitine (CRN) with γ-butyrobetaine (GBB) across the bacterial membrane. Three structures have been resolved to date for CaiT, all in the inward-facing state: CRN-bound (with four CRNs per subunit), GBB-bound (two GBBs per subunit), and apo. One of the reported binding sites is the counterpart of the primary site observed in structurally similar transporters. However, the mechanism and pathway(s) of CRN/GBB unbinding and translocation, or even the ability of the substrates to dislodge from the reported binding sites, are yet to be determined. To shed light on these issues, we performed a total of 1.3 μs of molecular dynamics simulations and examined the dynamics of substrate-bound CaiT structures under different conditions. We find that both CRN and GBB are able to dissociate completely from their primary site into the cytoplasm. Substrate molecules initially located at the secondary sites dissociate even faster (within tens of nanoseconds) into the extra- or intracellular regions. Interestingly, the unbinding pathway from the primary site appears to be dictated by the geometry of the unwound part of the transmembrane (TM) helix 3, mostly around Thr100 therein. Arg262 on TM7, which apparently mimics the role of Na+ in CaiT structural homologues, plays a key role in triggering the dissociation of the substrate away from the primary site and guiding its release to the cytoplasm provided that the unwound part of TM3 switches from a shielding to a yielding pose.
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Affiliation(s)
- Elia Zomot
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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Abstract
Sponges harbour complex communities of diverse microorganisms, which have been postulated to form intimate symbiotic relationships with their host. Here we unravel some of these interactions by characterising the functional features of the microbial community of the sponge Cymbastela concentrica through a combined metagenomic and metaproteomic approach. We discover the expression of specific transport functions for typical sponge metabolites (for example, halogenated aromatics, dipeptides), which indicates metabolic interactions between the community and the host. We also uncover the simultaneous performance of aerobic nitrification and anaerobic denitrification, which would aid to remove ammonium secreted by the sponge. Our analysis also highlights the requirement for the microbial community to respond to variable environmental conditions and hence express an array of stress protection proteins. Molecular interactions between symbionts and their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators. Finally, some sponge-associated bacteria (for example, a Phyllobacteriaceae phylotype) appear to undergo an evolutionary adaptation process to the sponge environment as evidenced by active mobile genetic elements. Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities.
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Talibart R, Jebbar M, Gouffi K, Pichereau V, Gouesbet G, Blanco C, Bernard T, Pocard J. Transient Accumulation of Glycine Betaine and Dynamics of Endogenous Osmolytes in Salt-Stressed Cultures of Sinorhizobium meliloti. Appl Environ Microbiol 2010; 63:4657-63. [PMID: 16535748 PMCID: PMC1389304 DOI: 10.1128/aem.63.12.4657-4663.1997] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fate of exogenously supplied glycine betaine and the dynamics of endogenous osmolytes were investigated throughout the growth cycle of salt-stressed cultures of strains of Sinorhizobium meliloti which differ in their ability to use glycine betaine as a growth substrate, but not as an osmoprotectant. We present (sup13)C nuclear magnetic resonance spectral and radiotracer evidence which demonstrates that glycine betaine is only transiently accumulated as a cytoplasmic osmolyte in young cultures of wild-type strains 102F34 and RCR2011. Specifically, these strains accumulate glycine betaine as a preferred osmolyte which virtually prevents the accumulation of endogenous osmolytes during the lag and early exponential phases of growth. Then, betaine levels in stressed cells decrease abruptly during the second half of the exponential phase. At this stage, the levels of glutamate and the dipeptide N-acetylglutaminylglutamine amide increase sharply so that the two endogenous solutes supplant glycine betaine in the ageing culture, in which it becomes a minor osmolyte because it is progressively catabolized. Ultimately, glycine betaine disappears when stressed cells reach the stationary phase. At this stage, wild-type strains of S. meliloti also accumulate the disaccharide trehalose as a third major endogenous osmolyte. By contrast, glycine betaine is always the dominant osmolyte and strongly suppresses the buildup of endogenous osmolytes at all stages of the growth cycle of a mutant strain, S. meliloti GMI766, which does not catabolize this exogenous osmoprotectant under any growth conditions.
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Tang L, Bai L, Wang WH, Jiang T. Crystal structure of the carnitine transporter and insights into the antiport mechanism. Nat Struct Mol Biol 2010; 17:492-6. [DOI: 10.1038/nsmb.1788] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 02/17/2010] [Indexed: 11/09/2022]
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Biofilm growth kinetics of a monomethylamine producing Alphaproteobacteria strain isolated from an anaerobic reactor. Anaerobe 2010; 16:19-26. [DOI: 10.1016/j.anaerobe.2009.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 04/23/2009] [Accepted: 04/29/2009] [Indexed: 11/17/2022]
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Hormiga J, González-Alcón C, Sevilla A, Cánovas M, Torres NV. Quantitative analysis of the dynamic signaling pathway involved in the cAMP mediated induction of l-carnitine biosynthesis in E. coli cultures. MOLECULAR BIOSYSTEMS 2010; 6:699-710. [PMID: 20237648 DOI: 10.1039/b913063b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
L-(-)-carnitine can be synthesized from waste bioprecursors in the form of crotonobetaine. Such biotransformation is carried out in E. coli by the enzymes encoded by operons regulated by the cAMP receptor proteins. Non-phosphorylated sugars, such as glycerol are used as energy and carbon source since glucose inhibits cAMP synthesis. Until now little attention has been paid to the regulatory signaling structure that operates during the transition from a glucose-consuming, non-l-carnitine producing steady state, to a glycerol-consuming l-carnitine producing steady state. In this work we aim to elucidate and quantify the underlying regulatory mechanisms operating in the abolition of the glucose inhibiting effect. For this purpose we make use of the systemic approach by integrating the available information and our own experimentally generated data to construct a mathematical model. The model is built using power-law representation and is used as a platform to make predictive simulations and to assess the consistency of the regulatory structure of the overall process. The model is subsequently checked for quality through stability and a special, dynamic sensitivity analysis. The results show that the model is able to deal with the observed system transient phase. The model is multi-hierarchical, comprising the metabolic, gene expression, signaling and bioreactor levels. It involves variables and parameters of a very different nature that develop in different time scales and orders of magnitude. Some of the most relevant conclusions obtained are: (i) the regulatory interactions among glucose, glycerol and cAMP metabolism are far stronger than those present in the l-carnitine transport, production and degradation processes; (ii) carnitine biosynthesis is very sensitive to the cAMP signaling system since it reacts at very low cAMP receptor concentrations, and (iii) ATP is a critical factor in the transient dynamics. All these model-derived observations have been experimentally confirmed by separate studies. As a whole, the model contributes to our general understanding of the transient regulation through the signal regulatory structure, thus enabling more accurate optimization strategies to be used.
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Affiliation(s)
- José Hormiga
- Grupo de Tecnología Bioquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Biología, Universidad de La Laguna, 38206, La Laguna, Tenerife, Islas Canarias, Spain
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Cánovas M, Iborra J. Whole cell biocatalysts stabilization forl-carnitine production. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500219040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sevilla A, Vera J, Díaz Z, Cánovas M, Torres NV, Iborra JL. Design of Metabolic Engineering Strategies for Maximizing l-(-)-Carnitine Production by Escherichia coli. Integration of the Metabolic and Bioreactor Levels. Biotechnol Prog 2008; 21:329-37. [PMID: 15801767 DOI: 10.1021/bp0497583] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work metabolic engineering strategies for maximizing L-(-)-carnitine production by Escherichia coli based on the Biochemical System Theory and the Indirect Optimization Method are presented. The model integrates the metabolic and the bioreactor levels using power-law formalism. Based on the S-system model, the Indirect Optimization Method was applied, leading to profiles of parameter values that are compatible with both the physiology of the cells and the bioreactor system operating conditions. This guarantees their viability and fitness and yields higher rates of L-(-)-carnitine production. Experimental results using a high cell density reactor were compared with optimized predictions from the Indirect Optimization Method. When two parameters (the dilution rate and the initial crotonobetaine concentration) were directly changed in the real experimental system to the prescribed optimum values, the system showed better performance in L-(-)-carnitine production (74% increase in production rate), in close agreement with the model's predictions. The model shows control points at macroscopic (reactor operation) and microscopic (molecular) levels where conversion and productivity can be increased. In accordance with the optimized solution, the next logical step to improve the L-(-)-carnitine production rate will involve metabolic engineering of the E. coli strain by overexpressing the carnitine transferase, CaiB, activity and the protein carrier, CaiT, responsible for substrate and product transport in and out of the cell. By this means it is predicted production may be enhanced by up to three times the original value.
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Affiliation(s)
- A Sevilla
- Departamento de Bioquímica y Biología Molecular B, Facultad de Química, Universidad de Murcia, 30100 Murcia, España
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Bernal V, Arense P, Blatz V, Mandrand-Berthelot MA, Cánovas M, Iborra JL. Role of betaine:CoA ligase (CaiC) in the activation of betaines and the transfer of coenzyme A in Escherichia coli. J Appl Microbiol 2008; 105:42-50. [PMID: 18266698 DOI: 10.1111/j.1365-2672.2008.03740.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Characterization of the role of CaiC in the biotransformation of trimethylammonium compounds into l(-)-carnitine in Escherichia coli. METHODS AND RESULTS The caiC gene was cloned and overexpressed in E. coli and its effect on the production of l(-)-carnitine was analysed. Betaine:CoA ligase and CoA transferase activities were analysed in cell free extracts and products were studied by electrospray mass spectrometry (ESI-MS). Substrate specificity of the caiC gene product was high, reflecting the high specialization of the carnitine pathway. Although CoA-transferase activity was also detected in vitro, the main in vivo role of CaiC was found to be the synthesis of betainyl-CoAs. Overexpression of CaiC allowed the biotransformation of crotonobetaine to l(-)-carnitine to be enhanced nearly 20-fold, the yield reaching up to 30% (with growing cells). Higher yields were obtained using resting cells (up to 60%), even when d(+)-carnitine was used as substrate. CONCLUSIONS The expression of CaiC is a control step in the biotransformation of trimethylammonium compounds in E. coli. SIGNIFICANCE AND IMPACT OF THE STUDY A bacterial betaine:CoA ligase has been characterized for the first time, underlining its important role for the production of l-carnitine with Escherichia coli.
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Affiliation(s)
- V Bernal
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Murcia, Spain
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Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J Bacteriol 2007; 190:2690-9. [PMID: 17951379 DOI: 10.1128/jb.01393-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycine betaine (GB), which occurs freely in the environment and is an intermediate in the catabolism of choline and carnitine, can serve as a sole source of carbon or nitrogen in Pseudomonas aeruginosa. Twelve mutants defective in growth on GB as the sole carbon source were identified through a genetic screen of a nonredundant PA14 transposon mutant library. Further growth experiments showed that strains with mutations in two genes, gbcA (PA5410) and gbcB (PA5411), were capable of growth on dimethylglycine (DMG), a catabolic product of GB, but not on GB itself. Subsequent nuclear magnetic resonance (NMR) experiments with 1,2-(13)C-labeled choline indicated that these genes are necessary for conversion of GB to DMG. Similar experiments showed that strains with mutations in the dgcAB (PA5398-PA5399) genes, which exhibit homology to genes that encode other enzymes with demethylase activity, are required for the conversion of DMG to sarcosine. Mutant analyses and (13)C NMR studies also confirmed that the soxBDAG genes, predicted to encode a sarcosine oxidase, are required for sarcosine catabolism. Our screen also identified a predicted AraC family transcriptional regulator, encoded by gbdR (PA5380), that is required for growth on GB and DMG and for the induction of gbcA, gbcB, and dgcAB in response to GB or DMG. Mutants defective in the previously described gbt gene (PA3082) grew on GB with kinetics similar to those of the wild type in both the PAO1 and PA14 strain backgrounds. These studies provided important insight into both the mechanism and the regulation of the catabolism of GB in P. aeruginosa.
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Wikoff WR, Gangoiti JA, Barshop BA, Siuzdak G. Metabolomics identifies perturbations in human disorders of propionate metabolism. Clin Chem 2007; 53:2169-76. [PMID: 17951291 DOI: 10.1373/clinchem.2007.089011] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND We applied untargeted mass spectrometry-based metabolomics to the diseases methylmalonic acidemia (MMA) and propionic acidemia (PA). METHODS We used a screening platform that used untargeted, mass-based metabolomics of methanol-extracted plasma to find significantly different molecular features in human plasma samples from MMA and PA patients and from healthy individuals. Capillary reverse phase liquid chromatography (4 microL/min) was interfaced to a TOF mass spectrometer, and data were processed using nonlinear alignment software (XCMS) and an online database (METLIN) to find and identify metabolites differentially regulated in disease. RESULTS Of the approximately 3500 features measured, propionyl carnitine was easily identified as the best biomarker of disease (P value 1.3 x 10(-18)), demonstrating the proof-of-concept use of untargeted metabolomics in clinical chemistry discovery. Five additional acylcarnitine metabolites showed significant differentiation between plasma from patients and healthy individuals, and gamma-butyrobetaine was highly increased in a subset of patients. Two acylcarnitine metabolites and numerous unidentified species differentiate MMA and PA. Many metabolites that do not appear in any public database, and that remain unidentified, varied significantly between normal, MMA, and PA, underscoring the complex downstream metabolic effects resulting from the defect in a single enzyme. CONCLUSIONS This proof-of-concept study demonstrates that metabolomics can expand the range of metabolites associated with human disease and shows that this method may be useful for disease diagnosis and patient clinical evaluation.
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Affiliation(s)
- William R Wikoff
- Department of Molecular Biology and The Center for Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92037, USA
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Bernal V, Sevilla Á, Cánovas M, Iborra JL. Production of L-carnitine by secondary metabolism of bacteria. Microb Cell Fact 2007; 6:31. [PMID: 17910757 PMCID: PMC2131755 DOI: 10.1186/1475-2859-6-31] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 10/02/2007] [Indexed: 11/25/2022] Open
Abstract
The increasing commercial demand for L-carnitine has led to a multiplication of efforts to improve its production with bacteria. The use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for L-carnitine production is discussed in the text. The different cell states of enterobacteria, such as Escherichia coli and Proteus sp., which can be used to produce L-carnitine from crotonobetaine or D-carnitine as substrate, are analyzed. Moreover, the combined application of both bioprocess and metabolic engineering has allowed a deeper understanding of the main factors controlling the production process, such as energy depletion and the alteration of the acetyl-CoA/CoA ratio which are coupled to the end of the biotransformation. Furthermore, the profiles of key central metabolic activities such as the TCA cycle, the glyoxylate shunt and the acetate metabolism are seen to be closely interrelated and affect the biotransformation efficiency. Although genetically modified strains have been obtained, new strain improvement strategies are still needed, especially in Escherichia coli as a model organism for molecular biology studies. This review aims to summarize and update the state of the art in L-carnitine production using E. coli and Proteus sp, emphasizing the importance of proper reactor design and operation strategies, together with metabolic engineering aspects and the need for feed-back between wet and in silico work to optimize this biotransformation.
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Affiliation(s)
- Vicente Bernal
- Department of Biochemistry and Molecular Biology B and Immunology, Campus of Espinardo, University of Murcia, E-30100, Spain
| | - Ángel Sevilla
- Department of Biochemistry and Molecular Biology B and Immunology, Campus of Espinardo, University of Murcia, E-30100, Spain
| | - Manuel Cánovas
- Department of Biochemistry and Molecular Biology B and Immunology, Campus of Espinardo, University of Murcia, E-30100, Spain
| | - José L Iborra
- Department of Biochemistry and Molecular Biology B and Immunology, Campus of Espinardo, University of Murcia, E-30100, Spain
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