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Jindal J, Hill J, Harte J, Dunachie SJ, Kronsteiner B. Starvation and infection: The role of sickness-associated anorexia in metabolic adaptation during acute infection. Metabolism 2024; 161:156035. [PMID: 39326837 DOI: 10.1016/j.metabol.2024.156035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 09/13/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024]
Abstract
Sickness-associated anorexia, the reduction in appetite seen during infection, is a widely conserved and well-recognized symptom of acute infection, yet there is very little understanding of its functional role in recovery. Anorexic sickness behaviours can be understood as an evolutionary strategy to increase tolerance to pathogen-mediated illness. In this review we explore the evidence for mechanisms and potential metabolic benefits of sickness-associated anorexia. Energy intake can impact on the immune response, control of inflammation and tissue stress, and on pathogen fitness. Fasting mediators including hormone-sensitive lipase, peroxisome proliferator-activated receptor-alpha (PPAR-α) and ketone bodies are potential facilitators of infection recovery through multiple pathways including suppression of inflammation, adaptation to lipid utilising pathways, and resistance to pathogen-induced cellular stress. However, the effect and benefit of calorie restriction is highly heterogeneous depending on both the infection and the metabolic status of the host, which has implications regarding clinical recommendations for feeding during different infections.
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Affiliation(s)
- Jessy Jindal
- The Medical School, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Jennifer Hill
- NDM Centre for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jodie Harte
- NDM Centre for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NDM Centre for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Barbara Kronsteiner
- NDM Centre for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK.
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2
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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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3
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Han M, Schierstaedt J, Duan Y, Nietschke M, Jechalke S, Wolf J, Hensel M, Neumann-Schaal M, Schikora A. Salmonella enterica relies on carbon metabolism to adapt to agricultural environments. Front Microbiol 2023; 14:1213016. [PMID: 37744895 PMCID: PMC10513388 DOI: 10.3389/fmicb.2023.1213016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/11/2023] [Indexed: 09/26/2023] Open
Abstract
Salmonella enterica, a foodborne and human pathogen, is a constant threat to human health. Agricultural environments, for example, soil and plants, can be ecological niches and vectors for Salmonella transmission. Salmonella persistence in such environments increases the risk for consumers. Therefore, it is necessary to investigate the mechanisms used by Salmonella to adapt to agricultural environments. We assessed the adaptation strategy of S. enterica serovar Typhimurium strain 14028s to agricultural-relevant situations by analyzing the abundance of intermediates in glycolysis and the tricarboxylic acid pathway in tested environments (diluvial sand soil suspension and leaf-based media from tomato and lettuce), as well as in bacterial cells grown in such conditions. By reanalyzing the transcriptome data of Salmonella grown in those environments and using an independent RT-qPCR approach for verification, several genes were identified as important for persistence in root or leaf tissues, including the pyruvate dehydrogenase subunit E1 encoding gene aceE. In vivo persistence assay in tomato leaves confirmed the crucial role of aceE. A mutant in another tomato leaf persistence-related gene, aceB, encoding malate synthase A, displayed opposite persistence features. By comparing the metabolites and gene expression of the wild-type strain and its aceB mutant, fumarate accumulation was discovered as a potential way to replenish the effects of the aceB mutation. Our research interprets the mechanism of S. enterica adaptation to agriculture by adapting its carbon metabolism to the carbon sources available in the environment. These insights may assist in the development of strategies aimed at diminishing Salmonella persistence in food production systems.
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Affiliation(s)
- Min Han
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jasper Schierstaedt
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Department Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Yongming Duan
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Monika Nietschke
- Division of Microbiology, Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Sven Jechalke
- Institute of Phytopathology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus-Liebig-University Gießen, Gießen, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Hensel
- Division of Microbiology, Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Adam Schikora
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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4
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Mitosch K, Beyß M, Phapale P, Drotleff B, Nöh K, Alexandrov T, Patil KR, Typas A. A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella. PLoS Biol 2023; 21:e3002198. [PMID: 37594988 PMCID: PMC10468081 DOI: 10.1371/journal.pbio.3002198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/30/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023] Open
Abstract
Pathogenic bacteria proliferating inside mammalian host cells need to rapidly adapt to the intracellular environment. How they achieve this and scavenge essential nutrients from the host has been an open question due to the difficulties in distinguishing between bacterial and host metabolites in situ. Here, we capitalized on the inability of mammalian cells to metabolize mannitol to develop a stable isotopic labeling approach to track Salmonella enterica metabolites during intracellular proliferation in host macrophage and epithelial cells. By measuring label incorporation into Salmonella metabolites with liquid chromatography-mass spectrometry (LC-MS), and combining it with metabolic modeling, we identify relevant carbon sources used by Salmonella, uncover routes of their metabolization, and quantify relative reaction rates in central carbon metabolism. Our results underline the importance of the Entner-Doudoroff pathway (EDP) and the phosphoenolpyruvate carboxylase for intracellularly proliferating Salmonella. More broadly, our metabolic labeling strategy opens novel avenues for understanding the metabolism of pathogens inside host cells.
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Affiliation(s)
- Karin Mitosch
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- RWTH Aachen University, Computational Systems Biotechnology, Aachen, Germany
| | - Prasad Phapale
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bernhard Drotleff
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Theodore Alexandrov
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- BioInnovation Institute, Copenhagen, Denmark
| | - Kiran R. Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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5
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Zhang Y, Chen R, Zhang D, Qi S, Liu Y. Metabolite interactions between host and microbiota during health and disease: Which feeds the other? Biomed Pharmacother 2023; 160:114295. [PMID: 36709600 DOI: 10.1016/j.biopha.2023.114295] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Metabolites produced by the host and microbiota play a crucial role in how human bodies develop and remain healthy. Most of these metabolites are produced by microbiota and hosts in the digestive tract. Metabolites in the gut have important roles in energy metabolism, cellular communication, and host immunity, among other physiological activities. Although numerous host metabolites, such as free fatty acids, amino acids, and vitamins, are found in the intestine, metabolites generated by gut microbiota are equally vital for intestinal homeostasis. Furthermore, microbiota in the gut is the sole source of some metabolites, including short-chain fatty acids (SCFAs). Metabolites produced by microbiota, such as neurotransmitters and hormones, may modulate and significantly affect host metabolism. The gut microbiota is becoming recognized as a second endocrine system. A variety of chronic inflammatory disorders have been linked to aberrant host-microbiota interplays, but the precise mechanisms underpinning these disturbances and how they might lead to diseases remain to be fully elucidated. Microbiome-modulated metabolites are promising targets for new drug discovery due to their endocrine function in various complex disorders. In humans, metabolotherapy for the prevention or treatment of various disorders will be possible if we better understand the metabolic preferences of bacteria and the host in specific tissues and organs. Better disease treatments may be possible with the help of novel complementary therapies that target host or bacterial metabolism. The metabolites, their physiological consequences, and functional mechanisms of the host-microbiota interplays will be highlighted, summarized, and discussed in this overview.
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Affiliation(s)
- Yan Zhang
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Rui Chen
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - DuoDuo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China.
| | - Shuang Qi
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Yan Liu
- Department of Hand and Foot Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
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6
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Shi F, Liu G, Lin Y, Guo CL, Han J, Chu ESH, Shi C, Li Y, Zhang H, Hu C, Liu R, He S, Guo G, Chen Y, Zhang X, Coker OO, Wong SH, Yu J, She J. Altered gut microbiome composition by appendectomy contributes to colorectal cancer. Oncogene 2023; 42:530-540. [PMID: 36539569 PMCID: PMC9918431 DOI: 10.1038/s41388-022-02569-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut microbial dysbiosis. Population-based longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases throughout 20 years follow-up (Adjusted sub-distribution hazard ratio (SHR) 1.73, 95% CI 1.49-2.01, P < 0.001). Shotgun metagenomic sequencing was performed on fecal samples from cohort 2 (n = 314). Gut microbial dysbiosis in appendectomy subjects was observed with significant enrichment of 7 CRC-promoting bacteria (Bacteroides vulgatus, Bacteroides fragilis, Veillonella dispar, Prevotella ruminicola, Prevotella fucsa, Prevotella dentalis, Prevotella denticola) and depletion of 5 beneficial commensals (Blautia sp YL58, Enterococcus hirae, Lachnospiraceae bacterium Choco86, Collinsella aerofaciens, Blautia sp SC05B48). Microbial network analysis showed increased correlation strengths among enriched bacteria and their enriched oncogenic pathways in appendectomy subjects compared to controls. Of which, B. fragilis was the centrality in the network of the enriched bacteria. We further confirmed that appendectomy promoted colorectal tumorigenesis in mice by causing gut microbial dysbiosis and impaired intestinal barrier function. Collectively, this study revealed appendectomy-induced microbial dysbiosis characterized by enriched CRC-promoting bacteria and depleted beneficial commensals, signifying that the gut microbiome may play a crucial role in CRC development induced by appendectomy.
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Affiliation(s)
- Feiyu Shi
- grid.452438.c0000 0004 1760 8119Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China ,grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Gaixia Liu
- grid.452438.c0000 0004 1760 8119Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China ,grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Yufeng Lin
- grid.10784.3a0000 0004 1937 0482State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Cosmos liutao Guo
- grid.10784.3a0000 0004 1937 0482State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jing Han
- grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Eagle S. H. Chu
- grid.10784.3a0000 0004 1937 0482State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chengxin Shi
- grid.452438.c0000 0004 1760 8119Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China ,grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Yaguang Li
- grid.452438.c0000 0004 1760 8119Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China ,grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Haowei Zhang
- grid.452438.c0000 0004 1760 8119Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China ,grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Chenhao Hu
- grid.452438.c0000 0004 1760 8119Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China ,grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Ruihan Liu
- grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Shuixiang He
- grid.452438.c0000 0004 1760 8119Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Gang Guo
- grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Yinnan Chen
- grid.43169.390000 0001 0599 1243Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi’an Jiao tong University, Xi’an, Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Xiang Zhang
- grid.10784.3a0000 0004 1937 0482State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Olabisi Oluwabukola Coker
- grid.10784.3a0000 0004 1937 0482State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sunny Hei Wong
- grid.10784.3a0000 0004 1937 0482State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiao tong University, Xi'an, Shaanxi, China. .,State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Junjun She
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiao tong University, Xi'an, Shaanxi, China. .,Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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7
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Dual transcriptome based reconstruction of Salmonella-human integrated metabolic network to screen potential drug targets. PLoS One 2022; 17:e0268889. [PMID: 35609089 PMCID: PMC9129043 DOI: 10.1371/journal.pone.0268889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a highly adaptive pathogenic bacteria with a serious public health concern due to its increasing resistance to antibiotics. Therefore, identification of novel drug targets for S. Typhimurium is crucial. Here, we first created a pathogen-host integrated genome-scale metabolic network by combining the metabolic models of human and S. Typhimurium, which we further tailored to the pathogenic state by the integration of dual transcriptome data. The integrated metabolic model enabled simultaneous investigation of metabolic alterations in human cells and S. Typhimurium during infection. Then, we used the tailored pathogen-host integrated genome-scale metabolic network to predict essential genes in the pathogen, which are candidate novel drug targets to inhibit infection. Drug target prioritization procedure was applied to these targets, and pabB was chosen as a putative drug target. It has an essential role in 4-aminobenzoic acid (PABA) synthesis, which is an essential biomolecule for many pathogens. A structure based virtual screening was applied through docking simulations to predict candidate compounds that eliminate S. Typhimurium infection by inhibiting pabB. To our knowledge, this is the first comprehensive study for predicting drug targets and drug like molecules by using pathogen-host integrated genome-scale models, dual RNA-seq data and structure-based virtual screening protocols. This framework will be useful in proposing novel drug targets and drugs for antibiotic-resistant pathogens.
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8
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Abstract
Accumulation of phosphorylated intermediates during cellular metabolism can have wide-ranging toxic effects on many organisms, including humans and the pathogens that infect them. These toxicities can be induced by feeding an upstream metabolite (a sugar, for instance) while simultaneously blocking the appropriate metabolic pathway with either a mutation or an enzyme inhibitor. Here, we survey the toxicities that can arise in the metabolism of glucose, galactose, fructose, fructose-asparagine, glycerol, trehalose, maltose, mannose, mannitol, arabinose, and rhamnose. Select enzymes in these metabolic pathways may serve as novel therapeutic targets. Some are conserved broadly among prokaryotes and eukaryotes (e.g., glucose and galactose) and are therefore unlikely to be viable drug targets. However, others are found only in bacteria (e.g., fructose-asparagine, rhamnose, and arabinose), and one is found in fungi but not in humans (trehalose). We discuss what is known about the mechanisms of toxicity and how resistance is achieved in order to identify the prospects and challenges associated with targeted exploitation of these pervasive metabolic vulnerabilities.
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9
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Persistence of Intracellular Bacterial Pathogens-With a Focus on the Metabolic Perspective. Front Cell Infect Microbiol 2021; 10:615450. [PMID: 33520740 PMCID: PMC7841308 DOI: 10.3389/fcimb.2020.615450] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
Persistence has evolved as a potent survival strategy to overcome adverse environmental conditions. This capability is common to almost all bacteria, including all human bacterial pathogens and likely connected to chronic infections caused by some of these pathogens. Although the majority of a bacterial cell population will be killed by the particular stressors, like antibiotics, oxygen and nitrogen radicals, nutrient starvation and others, a varying subpopulation (termed persisters) will withstand the stress situation and will be able to revive once the stress is removed. Several factors and pathways have been identified in the past that apparently favor the formation of persistence, such as various toxin/antitoxin modules or stringent response together with the alarmone (p)ppGpp. However, persistence can occur stochastically in few cells even of stress-free bacterial populations. Growth of these cells could then be induced by the stress conditions. In this review, we focus on the persister formation of human intracellular bacterial pathogens, some of which belong to the most successful persister producers but lack some or even all of the assumed persistence-triggering factors and pathways. We propose a mechanism for the persister formation of these bacterial pathogens which is based on their specific intracellular bipartite metabolism. We postulate that this mode of metabolism ultimately leads, under certain starvation conditions, to the stalling of DNA replication initiation which may be causative for the persister state.
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Affiliation(s)
- Wolfgang Eisenreich
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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10
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Kehl A, Noster J, Hensel M. Eat in or Take out? Metabolism of Intracellular Salmonella enterica. Trends Microbiol 2020; 28:644-654. [DOI: 10.1016/j.tim.2020.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/15/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
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11
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Eisenreich W, Rudel T, Heesemann J, Goebel W. How Viral and Intracellular Bacterial Pathogens Reprogram the Metabolism of Host Cells to Allow Their Intracellular Replication. Front Cell Infect Microbiol 2019; 9:42. [PMID: 30886834 PMCID: PMC6409310 DOI: 10.3389/fcimb.2019.00042] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Viruses and intracellular bacterial pathogens (IBPs) have in common the need of suitable host cells for efficient replication and proliferation during infection. In human infections, the cell types which both groups of pathogens are using as hosts are indeed quite similar and include phagocytic immune cells, especially monocytes/macrophages (MOs/MPs) and dendritic cells (DCs), as well as nonprofessional phagocytes, like epithelial cells, fibroblasts and endothelial cells. These terminally differentiated cells are normally in a metabolically quiescent state when they are encountered by these pathogens during infection. This metabolic state of the host cells does not meet the extensive need for nutrients required for efficient intracellular replication of viruses and especially IBPs which, in contrast to the viral pathogens, have to perform their own specific intracellular metabolism to survive and efficiently replicate in their host cell niches. For this goal, viruses and IBPs have to reprogram the host cell metabolism in a pathogen-specific manner to increase the supply of nutrients, energy, and metabolites which have to be provided to the pathogen to allow its replication. In viral infections, this appears to be often achieved by the interaction of specific viral factors with central metabolic regulators, including oncogenes and tumor suppressors, or by the introduction of virus-specific oncogenes. Less is so far known on the mechanisms leading to metabolic reprogramming of the host cell by IBPs. However, the still scant data suggest that similar mechanisms may also determine the reprogramming of the host cell metabolism in IBP infections. In this review, we summarize and compare the present knowledge on this important, yet still poorly understood aspect of pathogenesis of human viral and especially IBP infections.
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Affiliation(s)
- Wolfgang Eisenreich
- Chair of Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany
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12
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Correia DM, Sargo CR, Silva AJ, Santos ST, Giordano RC, Ferreira EC, Zangirolami TC, Ribeiro MPA, Rocha I. Mapping Salmonella typhimurium pathways using 13C metabolic flux analysis. Metab Eng 2019; 52:303-314. [PMID: 30529284 DOI: 10.1016/j.ymben.2018.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022]
Abstract
In the last years, Salmonella has been extensively studied not only due to its importance as a pathogen, but also as a host to produce pharmaceutical compounds. However, the full exploitation of Salmonella as a platform for bioproduct delivery has been hampered by the lack of information about its metabolism. Genome-scale metabolic models can be valuable tools to delineate metabolic engineering strategies as long as they closely represent the actual metabolism of the target organism. In the present study, a 13C-MFA approach was applied to map the fluxes at the central carbon pathways of S. typhimurium LT2 growing at glucose-limited chemostat cultures. The experiments were carried out in a 2L bioreactor, using defined medium enriched with 20% 13C-labeled glucose. Metabolic flux distributions in central carbon pathways of S. typhimurium LT2 were estimated using OpenFLUX2 based on the labeling pattern of biomass protein hydrolysates together with biomass composition. The results suggested that pentose phosphate is used to catabolize glucose, with minor fluxes through glycolysis. In silico simulations, using Optflux and pFBA as simulation method, allowed to study the performance of the genome-scale metabolic model. In general, the accuracy of in silico simulations was improved by the superimposition of estimated intracellular fluxes to the existing genome-scale metabolic model, showing a better fitting to the experimental extracellular fluxes, whereas the intracellular fluxes of pentose phosphate and anaplerotic reactions were poorly described.
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Affiliation(s)
- Daniela M Correia
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Cintia R Sargo
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Adilson J Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Sophia T Santos
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga 4710-057, Portugal
| | - Roberto C Giordano
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Eugénio C Ferreira
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga 4710-057, Portugal
| | - Teresa C Zangirolami
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Marcelo P A Ribeiro
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Isabel Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga 4710-057, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
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13
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Heuner K, Kunze M, Chen F, Eisenreich W. The Pathometabolism of Legionella Studied by Isotopologue Profiling. Methods Mol Biol 2019; 1921:21-44. [PMID: 30694483 DOI: 10.1007/978-1-4939-9048-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metabolic pathways and fluxes can be analyzed under in vivo conditions by incorporation experiments using general 13C-labelled precursors. On the basis of the isotopologue compositions in amino acids or other metabolites, the incorporation rates of the supplied precursors and the pathways of their utilization can be studied in considerable detail. In this chapter, the method of isotopologue profiling is illustrated with recent work on the metabolism of intracellular living Legionella pneumophila.
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Affiliation(s)
- Klaus Heuner
- Robert Koch-Institut, ZBS 2, Working Group "Cellular Interactions of Bacterial Pathogens", Berlin, Germany.
| | - Mareike Kunze
- Robert Koch-Institut, ZBS 2, Working Group "Cellular Interactions of Bacterial Pathogens", Berlin, Germany
| | - Fan Chen
- Lehrstuhl für Biochemie, Technische Universität München, Garching, Germany
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14
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Radlinski LC, Brunton J, Steele S, Taft-Benz S, Kawula TH. Defining the Metabolic Pathways and Host-Derived Carbon Substrates Required for Francisella tularensis Intracellular Growth. mBio 2018; 9:e01471-18. [PMID: 30459188 PMCID: PMC6247087 DOI: 10.1128/mbio.01471-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022] Open
Abstract
Francisella tularensis is a Gram-negative, facultative, intracellular bacterial pathogen and one of the most virulent organisms known. A hallmark of F. tularensis pathogenesis is the bacterium's ability to replicate to high densities within the cytoplasm of infected cells in over 250 known host species, including humans. This demonstrates that F. tularensis is adept at modulating its metabolism to fluctuating concentrations of host-derived nutrients. The precise metabolic pathways and nutrients utilized by F. tularensis during intracellular growth, however, are poorly understood. Here, we use systematic mutational analysis to identify the carbon catabolic pathways and host-derived nutrients required for F. tularensis intracellular replication. We demonstrate that the glycolytic enzyme phosphofructokinase (PfkA), and thus glycolysis, is dispensable for F. tularensis SchuS4 virulence, and we highlight the importance of the gluconeogenic enzyme fructose 1,6-bisphosphatase (GlpX). We found that the specific gluconeogenic enzymes that function upstream of GlpX varied based on infection model, indicating that F. tularensis alters its metabolic flux according to the nutrients available within its replicative niche. Despite this flexibility, we found that glutamate dehydrogenase (GdhA) and glycerol 3-phosphate (G3P) dehydrogenase (GlpA) are essential for F. tularensis intracellular replication in all infection models tested. Finally, we demonstrate that host cell lipolysis is required for F. tularensis intracellular proliferation, suggesting that host triglyceride stores represent a primary source of glycerol during intracellular replication. Altogether, the data presented here reveal common nutritional requirements for a bacterium that exhibits characteristic metabolic flexibility during infection.IMPORTANCE The widespread onset of antibiotic resistance prioritizes the need for novel antimicrobial strategies to prevent the spread of disease. With its low infectious dose, broad host range, and high rate of mortality, F. tularensis poses a severe risk to public health and is considered a potential agent for bioterrorism. F. tularensis reaches extreme densities within the host cell cytosol, often replicating 1,000-fold in a single cell within 24 hours. This remarkable rate of growth demonstrates that F. tularensis is adept at harvesting and utilizing host cell nutrients. However, like most intracellular pathogens, the types of nutrients utilized by F. tularensis and how they are acquired is not fully understood. Identifying the essential pathways for F. tularensis replication may reveal new therapeutic strategies for targeting this highly infectious pathogen and may provide insight for improved targeting of intracellular pathogens in general.
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Affiliation(s)
- Lauren C Radlinski
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason Brunton
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shaun Steele
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA
| | - Sharon Taft-Benz
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Thomas H Kawula
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA
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15
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Thompson A, Fulde M, Tedin K. The metabolic pathways utilized by Salmonella Typhimurium during infection of host cells. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:140-154. [PMID: 29411544 DOI: 10.1111/1758-2229.12628] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
Only relatively recently has research on the metabolism of intracellular bacterial pathogens within their host cells begun to appear in the published literature. This reflects in part the experimental difficulties encountered in separating host metabolic processes from those of the resident pathogen. One of the most genetically tractable and thoroughly studied intracellular bacterial pathogens, Salmonella enterica serovar Typhimurium (S. Typhimurium), has been at the forefront of metabolic studies within eukaryotic host cells. In this review, we offer a synthesis of what has been discovered to date regarding the metabolic adaptation of S. Typhimurium to survival and growth within the infected host. We discuss many studies in the context of techniques used, types of host cells, how host metabolites contribute to intracellular survival and proliferation of the pathogen and how bacterial metabolism affects the virulence and persistence of the pathogen.
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Affiliation(s)
- Arthur Thompson
- Institute for Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Marcus Fulde
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany
| | - Karsten Tedin
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany
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16
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Cesur MF, Abdik E, Güven-Gülhan Ü, Durmuş S, Çakır T. Computational Systems Biology of Metabolism in Infection. EXPERIENTIA SUPPLEMENTUM (2012) 2018; 109:235-282. [PMID: 30535602 DOI: 10.1007/978-3-319-74932-7_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A systems approach to elucidate the effect of infection on cell metabolism provides several opportunities from a better understanding of molecular mechanisms to the identification of potential biomarkers and drug targets. This is obvious from the fact that we have witnessed the accelerated use of computational systems biology in the last five years to study metabolic changes in pathogen and/or host cells in response to infection. In this chapter, we aim to present a comprehensive review of the recent research by focusing on genome-scale metabolic network models of pathogen-host systems and genome-wide metabolomics and fluxomics analysis of infected cells.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ecehan Abdik
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ünzile Güven-Gülhan
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.
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17
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Bumann D, Schothorst J. Intracellular Salmonella metabolism. Cell Microbiol 2017; 19. [PMID: 28672057 DOI: 10.1111/cmi.12766] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/27/2017] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
Growth of Salmonella inside infected host cells is a key aspect of their ability to cause local enteritis or systemic disease. This growth depends on exploitation of host nutrients through a large Salmonella metabolism network with hundreds of metabolites and enzymes. Studies in cell culture infection models are unravelling more and more of the underlying molecular and cellular mechanisms but also show striking Salmonella metabolic plasticity depending on host cell line and experimental conditions. In vivo studies have revealed a qualitatively diverse, but quantitatively poor, host-Salmonella nutritional interface, which on one side makes Salmonella fitness largely resilient against metabolic perturbations, but on the other side severely limits Salmonella biomass generation and growth rates. This review discusses goals and techniques for studying Salmonella intracellular metabolism, summarises main results and implications, and proposes key issues that could be addressed in future studies.
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Affiliation(s)
- Dirk Bumann
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Joep Schothorst
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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18
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Suryanarayanan TS, Thirunavukkarasu N. Endolichenic fungi: the lesser known fungal associates of lichens. Mycology 2017; 8:189-196. [PMID: 30123639 PMCID: PMC6059131 DOI: 10.1080/21501203.2017.1352048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Lichens are the result of a stable mutualism between a fungal and a photosynthesising partner (alga or cyanobacterium). In addition to the fungal partner in this mutualism, lichens are associated with endolichenic fungi which reside inside their thalli. The endolichenic fungi appear to have evolved with the lichen and many of them are a source of novel metabolites vested with unique bioactivities. There is very little information on the biology of endolichenic fungi and their interactions with the other components of a lichen microbiome. There is an urgent need to understand these aspects of endolichenic fungi such that their ecology and economic potential are known more completely. The current knowledge on endolichenic fungi is reviewed here.
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19
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Eisenreich W, Rudel T, Heesemann J, Goebel W. To Eat and to Be Eaten: Mutual Metabolic Adaptations of Immune Cells and Intracellular Bacterial Pathogens upon Infection. Front Cell Infect Microbiol 2017; 7:316. [PMID: 28752080 PMCID: PMC5508010 DOI: 10.3389/fcimb.2017.00316] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
Intracellular bacterial pathogens (IBPs) invade and replicate in different cell types including immune cells, in particular of the innate immune system (IIS) during infection in the acute phase. However, immune cells primarily function as essential players in the highly effective and integrated host defense systems comprising the IIS and the adaptive immune system (AIS), which cooperatively protect the host against invading microbes including IBPs. As countermeasures, the bacterial pathogens (and in particular the IBPs) have developed strategies to evade or reprogram the IIS at various steps. The intracellular replication capacity and the anti-immune defense responses of the IBP's as well as the specific antimicrobial responses of the immune cells of the innate and the AIS depend on specific metabolic programs of the IBPs and their host cells. The metabolic programs of the immune cells supporting or counteracting replication of the IBPs appear to be mutually exclusive. Indeed, recent studies show that upon interaction of naïve, metabolically quiescent immune cells with IBPs, different metabolic activation processes occur which may result in the provision of a survival and replication niche for the pathogen or its eradication. It is therefore likely that within a possible host cell population subsets exist that are metabolically programmed for pro- or anti-microbial conditions. These metabolic programs may be triggered by the interactions between different bacterial agonistic components and host cell receptors. In this review, we summarize the current status in the field and discuss metabolic adaptation processes within immune cells of the IIS and the IBPs that support or restrict the intracellular replication of the pathogens.
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Affiliation(s)
- Wolfgang Eisenreich
- Department of Chemistry, Chair of Biochemistry, Technische Universität MünchenGarching, Germany
| | - Thomas Rudel
- Department of Microbiology, Biocenter, University of WürzburgWürzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Chair of Medical Microbiology and Hospital Epidemiology, Ludwig Maximilian University of MunichMünchen, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Chair of Medical Microbiology and Hospital Epidemiology, Ludwig Maximilian University of MunichMünchen, Germany
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20
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Diacovich L, Lorenzi L, Tomassetti M, Méresse S, Gramajo H. The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole. Virulence 2016; 8:975-992. [PMID: 27936347 DOI: 10.1080/21505594.2016.1270493] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that causes various host-specific diseases. During their life cycle, Salmonellae survive frequent exposures to a variety of environmental stresses, e.g. carbon-source starvation. The virulence of this pathogen relies on its ability to establish a replicative niche, named Salmonella-containing vacuole, inside host cells. However, the microenvironment of the SCV and the bacterial metabolic pathways required during infection are largely undefined. In this work we developed different biological probes whose expression is modulated by the environment and the physiological state of the bacterium. We constructed transcriptional reporters by fusing promoter regions to the gfpmut3a gene to monitor the expression profile of genes involved in glucose utilization and lipid catabolism. The induction of these probes by a specific metabolic change was first tested in vitro, and then during different conditions of infection in macrophages. We were able to determine that Entner-Doudoroff is the main metabolic pathway utilized by Salmonella during infection in mouse macrophages. Furthermore, we found sub-populations of bacteria expressing genes involved in pathways for the utilization of different sources of carbon. These populations are modified in presence of different metabolizable substrates, suggesting the coexistence of Salmonella with diverse metabolic states during the infection.
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Affiliation(s)
- Lautaro Diacovich
- a Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Rosario , Argentina
| | - Lucía Lorenzi
- a Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Rosario , Argentina
| | - Mauro Tomassetti
- a Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Rosario , Argentina
| | - Stéphane Méresse
- b Aix Marseille Université, CNRS, INSERM, CIML , Marseille , France
| | - Hugo Gramajo
- a Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Rosario , Argentina
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21
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Liu Y, Yu K, Zhou F, Ding T, Yang Y, Hu M, Liu X. Quantitative Proteomics Charts the Landscape of Salmonella Carbon Metabolism within Host Epithelial Cells. J Proteome Res 2016; 16:788-797. [DOI: 10.1021/acs.jproteome.6b00793] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yanhua Liu
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Kaiwen Yu
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fan Zhou
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tao Ding
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yufei Yang
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mo Hu
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry
and Synthetic and Functional Biomolecules Center, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
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22
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Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. Metab Eng 2016; 38:251-263. [PMID: 27637318 DOI: 10.1016/j.ymben.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/07/2016] [Accepted: 09/11/2016] [Indexed: 01/22/2023]
Abstract
Pseudomonas aeruginosa is a metabolically versatile wide-ranging opportunistic pathogen. In humans P. aeruginosa causes infections of the skin, urinary tract, blood, and the lungs of Cystic Fibrosis patients. In addition, P. aeruginosa's broad environmental distribution, relatedness to biotechnologically useful species, and ability to form biofilms have made it the focus of considerable interest. We used 13C metabolic flux analysis (MFA) and flux balance analysis to understand energy and redox production and consumption and to explore the metabolic phenotypes of one reference strain and five strains isolated from the lungs of cystic fibrosis patients. Our results highlight the importance of the oxidative pentose phosphate and Entner-Doudoroff pathways in P. aeruginosa growth. Among clinical strains we report two divergent metabolic strategies and identify changes between genetically related strains that have emerged during a chronic infection of the same patient. MFA revealed that the magnitude of fluxes through the glyoxylate cycle correlates with growth rates.
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23
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Metabolic Adaptations of Intracellullar Bacterial Pathogens and their Mammalian Host Cells during Infection ("Pathometabolism"). Microbiol Spectr 2016; 3. [PMID: 26185075 DOI: 10.1128/microbiolspec.mbp-0002-2014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several bacterial pathogens that cause severe infections in warm-blooded animals, including humans, have the potential to actively invade host cells and to efficiently replicate either in the cytosol or in specialized vacuoles of the mammalian cells. The interaction between these intracellular bacterial pathogens and the host cells always leads to multiple physiological changes in both interacting partners, including complex metabolic adaptation reactions aimed to promote proliferation of the pathogen within different compartments of the host cells. In this chapter, we discuss the necessary nutrients and metabolic pathways used by some selected cytosolic and vacuolar intracellular pathogens and--when available--the links between the intracellular bacterial metabolism and the expression of the virulence genes required for the intracellular bacterial replication cycle. Furthermore, we address the growing evidence that pathogen-specific factors may also trigger metabolic responses of the infected mammalian cells affecting the carbon and nitrogen metabolism as well as defense reactions. We also point out that many studies on the metabolic host cell responses induced by the pathogens have to be scrutinized due to the use of established cell lines as model host cells, as these cells are (in the majority) cancer cells that exhibit a dysregulated primary carbon metabolism. As the exact knowledge of the metabolic host cell responses may also provide new concepts for antibacterial therapies, there is undoubtedly an urgent need for host cell models that more closely reflect the in vivo infection conditions.
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24
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Thompson AP, O'Neill I, Smith EJ, Catchpole J, Fagan A, Burgess KEV, Carmody RJ, Clarke DJ. Glycolysis and pyrimidine biosynthesis are required for replication of adherent-invasive Escherichia coli in macrophages. MICROBIOLOGY-SGM 2016; 162:954-965. [PMID: 27058922 DOI: 10.1099/mic.0.000289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Adherent-invasive Escherichia coli (AIEC) have been implicated in the aetiology of Crohn's disease (CD), a chronic inflammatory bowel condition. It has been proposed that AIEC-infected macrophages produce high levels of pro-inflammatory cytokines thus contributing to the inflammation observed in CD. AIEC can replicate in macrophages and we wanted to determine if bacterial replication was linked to the high level of cytokine production associated with AIEC-infected macrophages. Therefore, we undertook a genetic analysis of the metabolic requirements for AIEC replication in the macrophage and we show that AIEC replication in this niche is dependent on bacterial glycolysis. In addition, our analyses indicate that AIEC have access to a wide range of nutrients in the macrophage, although the levels of purines and pyrimidines do appear to be limiting. Finally, we show that the macrophage response to AIEC infection is indistinguishable from the response to the non-replicating glycolysis mutant (ΔpfkAB) and a non-pathogenic strain of E. coli, MG1655. Therefore, AIEC does not appear to subvert the normal macrophage response to E. coli during infection.
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Affiliation(s)
- Aoife P Thompson
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Ian O'Neill
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Emma J Smith
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - John Catchpole
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Ailis Fagan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Karl E V Burgess
- Glasgow Polyomics, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | | | - David J Clarke
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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25
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A Comparison of the ATP Generating Pathways Used by S. Typhimurium to Fuel Replication within Human and Murine Macrophage and Epithelial Cell Lines. PLoS One 2016; 11:e0150687. [PMID: 26930214 PMCID: PMC4773185 DOI: 10.1371/journal.pone.0150687] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/18/2016] [Indexed: 12/21/2022] Open
Abstract
The metabolism of S. Typhimurium within infected host cells plays a fundamental role in virulence since it enables intracellular proliferation and dissemination and affects the innate immune response. An essential requirement for the intracellular replication of S. Typhimurium is the need to regenerate ATP. The metabolic route used to fulfil this requirement is the subject of the present study. For infection models we used human and murine epithelial and macrophage cell lines. The epithelial cell lines were mICc12, a transimmortalised murine colon enterocyte cell line that shows many of the characteristics of a primary epithelial cell line, and HeLa cells. The model macrophage cell lines were THP-1A human monocyte/macrophages and RAW 264.7 murine macrophages. Using a mutational approach combined with an exometabolomic analysis, we showed that neither fermentative metabolism nor anaerobic respiration play major roles in energy generation in any of the cell lines studied. Rather, we identified overflow metabolism to acetate and lactate as the foremost route by which S. Typhimurium fulfils its energy requirements.
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26
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Role of host cell-derived amino acids in nutrition of intracellular Salmonella enterica. Infect Immun 2015; 83:4466-75. [PMID: 26351287 DOI: 10.1128/iai.00624-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022] Open
Abstract
The facultative intracellular pathogen Salmonella enterica resides in a specific membrane-bound compartment termed the Salmonella-containing vacuole (SCV). Despite being segregated from access to metabolites in the host cell cytosol, Salmonella is able to efficiently proliferate within the SCV. We set out to unravel the nutritional supply of Salmonella in the SCV with focus on amino acids. We studied the availability of amino acids by the generation of auxotrophic strains for alanine, asparagine, aspartate, glutamine, and proline in a macrophage cell line (RAW264.7) and an epithelial cell line (HeLa) and examined access to extracellular nutrients for nutrition. Auxotrophies for alanine, asparagine, or proline attenuated intracellular replication in HeLa cells, while aspartate, asparagine, or proline auxotrophies attenuated intracellular replication in RAW264.7 macrophages. The different patterns of intracellular attenuation of alanine- or aspartate-auxotrophic strains support distinct nutritional conditions in HeLa cells and RAW264.7 macrophages. Supplementation of medium with individual amino acids restored the intracellular replication of mutant strains auxotrophic for asparagine, proline, or glutamine. Similarly, a mutant strain deficient in succinate dehydrogenase was complemented by the extracellular addition of succinate. Complementation of the intracellular replication of auxotrophic Salmonella by external amino acids was possible if bacteria were proficient in the induction of Salmonella-induced filaments (SIFs) but failed in a SIF-deficient background. We propose that the ability of intracellular Salmonella to redirect host cell vesicular transport provides access of amino acids to auxotrophic strains and, more generally, is essential to continuously supply bacteria within the SCV with nutrients.
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27
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Sargo CR, Campani G, Silva GG, Giordano RC, Da Silva AJ, Zangirolami TC, Correia DM, Ferreira EC, Rocha I. Salmonella typhimurium and Escherichia coli dissimilarity: Closely related bacteria with distinct metabolic profiles. Biotechnol Prog 2015; 31:1217-25. [PMID: 26097206 DOI: 10.1002/btpr.2128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/20/2015] [Indexed: 01/17/2023]
Abstract
Live attenuated strains of Salmonella typhimurium have been extensively investigated as vaccines for a number of infectious diseases. However, there is still little information available concerning aspects of their metabolism. S. typhimurium and Escherichia coli show a high degree of similarity in terms of their genome contents and metabolic networks. However, this work presents experimental evidence showing that significant differences exist in their abilities to direct carbon fluxes to biomass and energy production. It is important to study the metabolism of Salmonella to elucidate the formation of acetate and other metabolites involved in optimizing the production of biomass, essential for the development of recombinant vaccines. The metabolism of Salmonella under aerobic conditions was assessed using continuous cultures performed at dilution rates ranging from 0.1 to 0.67 h(-1), with glucose as main substrate. Acetate assimilation and glucose metabolism under anaerobic conditions were also investigated using batch cultures. Chemostat cultivations showed deviation of carbon towards acetate formation, starting at dilution rates above 0.1 h(-1). This differed from previous findings for E. coli, where acetate accumulation was only detected at dilution rates exceeding 0.4 h(-1), and was due to the lower rate of acetate assimilation by S. typhimurium under aerobic conditions. Under anaerobic conditions, both microorganisms mainly produced ethanol, acetate, and formate. A genome-scale metabolic model, reconstructed for Salmonella based on an E. coli model, provided a poor description of the mixed fermentation pattern observed during Salmonella cultures, reinforcing the different patterns of carbon utilization exhibited by these closely related bacteria.
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Affiliation(s)
- Cintia R Sargo
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil
| | - Gilson Campani
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil
| | - Gabriel G Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil
| | - Roberto C Giordano
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil
| | - Adilson J Da Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil
| | - Teresa C Zangirolami
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil
| | - Daniela M Correia
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP, 13565-905,, Brazil.,CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga, 4710-057,, Portugal
| | - Eugénio C Ferreira
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga, 4710-057,, Portugal
| | - Isabel Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga, 4710-057,, Portugal
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Kreibich S, Hardt WD. Experimental approaches to phenotypic diversity in infection. Curr Opin Microbiol 2015; 27:25-36. [PMID: 26143306 DOI: 10.1016/j.mib.2015.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 12/16/2022]
Abstract
Microbial infections are burdening human health, even after the advent of antibiotics, vaccines and hygiene. Thus, infection biology has aimed at the molecular understanding of the pathogen-host interaction. This has revealed key virulence factors, host cell signaling pathways and immune responses. However, our understanding of the infection process is still incomplete. Recent evidence suggests that phenotypic diversity can have important consequences for the infection process. Diversity arises from the formation of distinct subpopulations of pathogen cells (with distinct virulence factor expression patterns) and host cells (with distinct response capacities). For technical reasons, such phenotypic diversity has often been overlooked. We are highlighting several striking examples and discuss the experimental approaches available for analyzing the different subpopulations. Single cell reporters and approaches from systems biology do hold much promise.
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Affiliation(s)
- Saskia Kreibich
- Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
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29
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Schunder E, Gillmaier N, Kutzner E, Eisenreich W, Herrmann V, Lautner M, Heuner K. Amino Acid Uptake and Metabolism of Legionella pneumophila Hosted by Acanthamoeba castellanii. J Biol Chem 2015; 289:21040-54. [PMID: 24904060 DOI: 10.1074/jbc.m114.570085] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Legionella pneumophila survives and replicates within a Legionella-containing vacuole (LCV) of amoebae and macrophages. Less is known about the carbon metabolism of the bacteria within the LCV. We have now analyzed the transfer and usage of amino acids from the natural host organism Acanthamoeba castellanii to Legionella pneumophila under in vivo (LCV) conditions. For this purpose, A. castellanii was 13C-labeled by incubation in buffer containing [U-(13)C(6)]glucose. Subsequently, these 13C-prelabeled amoebae were infected with L. pneumophila wild type or some mutants defective in putative key enzymes or regulators of carbon metabolism. 13C-Isotopologue compositions of amino acids from bacterial and amoebal proteins were then determined by mass spectrometry. In a comparative approach, the profiles documented the efficient uptake of Acanthamoeba amino acids into the LCV and further into L. pneumophila where they served as precursors for bacterial protein biosynthesis. More specifically, A. castellanii synthesized from exogenous [U-13C6]glucose unique isotopologue mixtures of several amino acids including Phe and Tyr, which were also observed in the same amino acids from LCV-grown L. pneumophila. Minor but significant differences were only detected in the isotopologue profiles of Ala, Asp, and Glu from the amoebal or bacterial protein fractions, respectively, indicating partial de novo synthesis of these amino acids by L. pneumophila. The similar isotopologue patterns in amino acids from L. pneumophila wild type and the mutants under study reflected the robustness of amino acid usage in the LCV of A. castellannii.
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30
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Dandekar T, Fieselmann A, Fischer E, Popp J, Hensel M, Noster J. Salmonella-how a metabolic generalist adopts an intracellular lifestyle during infection. Front Cell Infect Microbiol 2015; 4:191. [PMID: 25688337 PMCID: PMC4310325 DOI: 10.3389/fcimb.2014.00191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/21/2014] [Indexed: 12/12/2022] Open
Abstract
The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, "-omics" data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.
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Affiliation(s)
- Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Astrid Fieselmann
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Eva Fischer
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Jasmin Popp
- Division of Microbiology, Biology/Chemistry, University of Osnabrück Osnabrück, Germany
| | - Michael Hensel
- Division of Microbiology, Biology/Chemistry, University of Osnabrück Osnabrück, Germany
| | - Janina Noster
- Division of Microbiology, Biology/Chemistry, University of Osnabrück Osnabrück, Germany
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31
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Willenborg J, Huber C, Koczula A, Lange B, Eisenreich W, Valentin-Weigand P, Goethe R. Characterization of the pivotal carbon metabolism of Streptococcus suis serotype 2 under ex vivo and chemically defined in vitro conditions by isotopologue profiling. J Biol Chem 2015; 290:5840-54. [PMID: 25575595 DOI: 10.1074/jbc.m114.619163] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptococcus suis is a neglected zoonotic pathogen that has to adapt to the nutritional requirements in the different host niches encountered during infection and establishment of invasive diseases. To dissect the central metabolic activity of S. suis under different conditions of nutrient availability, we performed labeling experiments starting from [(13)C]glucose specimens and analyzed the resulting isotopologue patterns in amino acids of S. suis grown under in vitro and ex vivo conditions. In combination with classical growth experiments, we found that S. suis is auxotrophic for Arg, Gln/Glu, His, Leu, and Trp in chemically defined medium. De novo biosynthesis was shown for Ala, Asp, Ser, and Thr at high rates and for Gly, Lys, Phe, Tyr, and Val at moderate or low rates, respectively. Glucose degradation occurred mainly by glycolysis and to a minor extent by the pentose phosphate pathway. Furthermore, the exclusive formation of oxaloacetate by phosphoenolpyruvate (PEP) carboxylation became evident from the patterns in de novo synthesized amino acids. Labeling experiments with S. suis grown ex vivo in blood or cerebrospinal fluid reflected the metabolic adaptation to these host niches with different nutrient availability; however, similar key metabolic activities were identified under these conditions. This points at the robustness of the core metabolic pathways in S. suis during the infection process. The crucial role of PEP carboxylation for growth of S. suis in the host was supported by experiments with a PEP carboxylase-deficient mutant strain in blood and cerebrospinal fluid.
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Affiliation(s)
- Jörg Willenborg
- From the Institute of Microbiology, University of Veterinary Medicine Hannover, D-30173 Hannover, Germany and
| | - Claudia Huber
- the Lehrstuhl für Biochemie, Technische Universität München, D-85747 Garching, Germany
| | - Anna Koczula
- From the Institute of Microbiology, University of Veterinary Medicine Hannover, D-30173 Hannover, Germany and
| | - Birgit Lange
- the Lehrstuhl für Biochemie, Technische Universität München, D-85747 Garching, Germany
| | - Wolfgang Eisenreich
- the Lehrstuhl für Biochemie, Technische Universität München, D-85747 Garching, Germany
| | - Peter Valentin-Weigand
- From the Institute of Microbiology, University of Veterinary Medicine Hannover, D-30173 Hannover, Germany and
| | - Ralph Goethe
- From the Institute of Microbiology, University of Veterinary Medicine Hannover, D-30173 Hannover, Germany and
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32
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Lim S, Han A, Kim D, Seo HS. Transcriptional Profiling of an AttenuatedSalmonellaTyphimuriumptsIMutant Strain Under Low-oxygen Conditions using Microarray Analysis. ACTA ACUST UNITED AC 2015. [DOI: 10.4167/jbv.2015.45.3.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Ahreum Han
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Dongho Kim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Korea
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33
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Grubmüller S, Schauer K, Goebel W, Fuchs TM, Eisenreich W. Analysis of carbon substrates used by Listeria monocytogenes during growth in J774A.1 macrophages suggests a bipartite intracellular metabolism. Front Cell Infect Microbiol 2014; 4:156. [PMID: 25405102 PMCID: PMC4217532 DOI: 10.3389/fcimb.2014.00156] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023] Open
Abstract
Intracellular bacterial pathogens (IBPs) are dependent on various nutrients provided by the host cells. Different strategies may therefore be necessary to adapt the intracellular metabolism of IBPs to the host cells. The specific carbon sources, the catabolic pathways participating in their degradation, and the biosynthetic performances of IBPs are still poorly understood. In this report, we have exploited the technique of (13)C-isotopologue profiling to further study the carbon metabolism of Listeria monocytogenes by using the EGDe wild-type strain and mutants (defective in the uptake and/or catabolism of various carbon compounds) replicating in J774A.1 macrophages. For this goal, the infected macrophages were cultivated in the presence of [1,2-(13)C2]glucose, [U-(13)C3]glycerol, [U-(13)C3]pyruvate, [U-(13)C3]lactate, or a mix of [U-(13)C]amino acids. GC/MS-based isotopologue profiling showed efficient utilization of amino acids, glucose 6-phosphate, glycerol, and (at a low extent) also of lactate but not of pyruvate by the IBPs. Most amino acids imported from the host cells were directly used for bacterial protein biosynthesis and hardly catabolized. However, Asp was de novo synthesized by the IBPs and not imported from the host cell. As expected, glycerol was catabolized via the ATP-generating lower part of the glycolytic pathway, but apparently not used for gluconeogenesis. The intermediates generated from glucose 6-phosphate in the upper part of the glycolytic pathway and the pentose phosphate shunt likely serve primarily for anabolic purposes (probably for the biosynthesis of cell wall components and nucleotides). This bipartite bacterial metabolism which involves at least two major carbon substrates-glycerol mainly for energy supply and glucose 6-phosphate mainly for indispensible anabolic performances-may put less nutritional stress on the infected host cells, thereby extending the lifespan of the host cells to the benefit of the IBPs.
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Affiliation(s)
| | - Kristina Schauer
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Technische Universität München Freising, Germany
| | - Werner Goebel
- Department for Bacteriology, Max von Pettenkofer Institute, Ludwig-Maximilians-Universität München, Germany
| | - Thilo M Fuchs
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Technische Universität München Freising, Germany
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34
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Papenfort K, Vogel J. Small RNA functions in carbon metabolism and virulence of enteric pathogens. Front Cell Infect Microbiol 2014; 4:91. [PMID: 25077072 PMCID: PMC4098024 DOI: 10.3389/fcimb.2014.00091] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Enteric pathogens often cycle between virulent and saprophytic lifestyles. To endure these frequent changes in nutrient availability and composition bacteria possess an arsenal of regulatory and metabolic genes allowing rapid adaptation and high flexibility. While numerous proteins have been characterized with regard to metabolic control in pathogenic bacteria, small non-coding RNAs have emerged as additional regulators of metabolism. Recent advances in sequencing technology have vastly increased the number of candidate regulatory RNAs and several of them have been found to act at the interface of bacterial metabolism and virulence factor expression. Importantly, studying these riboregulators has not only provided insight into their metabolic control functions but also revealed new mechanisms of post-transcriptional gene control. This review will focus on the recent advances in this area of host-microbe interaction and discuss how regulatory small RNAs may help coordinate metabolism and virulence of enteric pathogens.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University Princeton, NJ, USA
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg Würzburg, Germany
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35
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Jelsbak L, Hartman H, Schroll C, Rosenkrantz JT, Lemire S, Wallrodt I, Thomsen LE, Poolman M, Kilstrup M, Jensen PR, Olsen JE. Identification of metabolic pathways essential for fitness of Salmonella Typhimurium in vivo. PLoS One 2014; 9:e101869. [PMID: 24992475 PMCID: PMC4081726 DOI: 10.1371/journal.pone.0101869] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/12/2014] [Indexed: 01/27/2023] Open
Abstract
Bacterial infections remain a threat to human and animal health worldwide, and there is an urgent need to find novel targets for intervention. In the current study we used a computer model of the metabolic network of Salmonella enterica serovar Typhimurium and identified pairs of reactions (cut sets) predicted to be required for growth in vivo. We termed such cut sets synthetic auxotrophic pairs. We tested whether these would reveal possible combined targets for new antibiotics by analyzing the performance of selected single and double mutants in systemic mouse infections. One hundred and two cut sets were identified. Sixty-three of these included only pathways encoded by fully annotated genes, and from this sub-set we selected five cut sets involved in amino acid or polyamine biosynthesis. One cut set (asnA/asnB) demonstrated redundancy in vitro and in vivo and showed that asparagine is essential for S. Typhimurium during infection. trpB/trpA as well as single mutants were attenuated for growth in vitro, while only the double mutant was a cut set in vivo, underlining previous observations that tryptophan is essential for successful outcome of infection. speB/speF,speC was not affected in vitro but was attenuated during infection showing that polyamines are essential for virulence apparently in a growth independent manner. The serA/glyA cut-set was found to be growth attenuated as predicted by the model. However, not only the double mutant, but also the glyA mutant, were found to be attenuated for virulence. This adds glycine production or conversion of glycine to THF to the list of essential reactions during infection. One pair (thrC/kbl) showed true redundancy in vitro but not in vivo demonstrating that threonine is available to the bacterium during infection. These data add to the existing knowledge of available nutrients in the intra-host environment, and have identified possible new targets for antibiotics.
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Affiliation(s)
- Lotte Jelsbak
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hassan Hartman
- Department of Medical and Biological Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, United Kingdom
| | - Casper Schroll
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jesper T. Rosenkrantz
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sebastien Lemire
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inke Wallrodt
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Line E. Thomsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mark Poolman
- Department of Medical and Biological Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, United Kingdom
| | - Mogens Kilstrup
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter R. Jensen
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - John E. Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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36
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Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proc Natl Acad Sci U S A 2014; 111:9929-34. [PMID: 24958876 DOI: 10.1073/pnas.1406694111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Shigella flexneri proliferate in infected human epithelial cells at exceptionally high rates. This vigorous growth has important consequences for rapid progression to life-threatening bloody diarrhea, but the underlying metabolic mechanisms remain poorly understood. Here, we used metabolomics, proteomics, and genetic experiments to determine host and Shigella metabolism during infection in a cell culture model. The data suggest that infected host cells maintain largely normal fluxes through glycolytic pathways, but the entire output of these pathways is captured by Shigella, most likely in the form of pyruvate. This striking strategy provides Shigella with an abundant favorable energy source, while preserving host cell ATP generation, energy charge maintenance, and survival, despite ongoing vigorous exploitation. Shigella uses a simple three-step pathway to metabolize pyruvate at high rates with acetate as an excreted waste product. The crucial role of this pathway for Shigella intracellular growth suggests targets for antimicrobial chemotherapy of this devastating disease.
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37
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Vázquez CL, Lerner TR, Kasmapour B, Pei G, Gronow A, Bianco MV, Blanco FC, Bleck CKE, Geffers R, Bigi F, Abraham WR, Gutierrez MG. Experimental selection of long-term intracellular mycobacteria. Cell Microbiol 2014; 16:1425-40. [PMID: 24779357 PMCID: PMC4283733 DOI: 10.1111/cmi.12303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 04/09/2014] [Accepted: 04/13/2014] [Indexed: 11/30/2022]
Abstract
Some intracellular bacteria are known to cause long-term infections that last decades without compromising the viability of the host. Although of critical importance, the adaptations that intracellular bacteria undergo during this long process of residence in a host cell environment remain obscure. Here, we report a novel experimental approach to study the adaptations of mycobacteria imposed by a long-term intracellular lifestyle. Selected Mycobacterium bovis BCG through continuous culture in macrophages underwent an adaptation process leading to impaired phenolic glycolipids (PGL) synthesis, improved usage of glucose as a carbon source and accumulation of neutral lipids. These changes correlated with increased survival of mycobacteria in macrophages and mice during re-infection and also with the specific expression of stress- and survival-related genes. Our findings identify bacterial traits implicated in the establishment of long-term cellular infections and represent a tool for understanding the physiological states and the environment that bacteria face living in fluctuating intracellular environments.
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Affiliation(s)
- Cristina L Vázquez
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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38
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Bowden SD, Hopper-Chidlaw AC, Rice CJ, Ramachandran VK, Kelly DJ, Thompson A. Nutritional and metabolic requirements for the infection of HeLa cells by Salmonella enterica serovar Typhimurium. PLoS One 2014; 9:e96266. [PMID: 24797930 PMCID: PMC4010460 DOI: 10.1371/journal.pone.0096266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 04/07/2014] [Indexed: 12/04/2022] Open
Abstract
Salmonella is the causative agent of a spectrum of human and animal diseases ranging from gastroenteritis to typhoid fever. It is a food - and water - borne pathogen and infects via ingestion followed by invasion of intestinal epithelial cells and phagocytic cells. In this study we employed a mutational approach to define the nutrients and metabolic pathways required by Salmonella enterica serovar Typhimurium during infection of a human epithelial cell line (HeLa). We deleted the key glycolytic genes, pfkA and pfkB to show that S. Typhimurium utilizes glycolysis for replication within HeLa cells; however, glycolysis was not absolutely essential for intracellular replication. Using S. Typhimurium strains deleted for genes encoding components of the phosphotransferase system and glucose transport, we show that glucose is a major substrate required for the intracellular replication of S. Typhimurium in HeLa cells. We also deleted genes encoding enzymes involved in the utilization of gluconeogenic substrates and the glyoxylate shunt and show that neither of these pathways were required for intracellular replication of S. Typhimurium within HeLa cells.
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Affiliation(s)
- Steven D. Bowden
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | | | | | - Vinoy K. Ramachandran
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- * E-mail:
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39
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Role of intracellular carbon metabolism pathways in Shigella flexneri virulence. Infect Immun 2014; 82:2746-55. [PMID: 24733092 DOI: 10.1128/iai.01575-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella flexneri, which replicates in the cytoplasm of intestinal epithelial cells, can use the Embden-Meyerhof-Parnas, Entner-Doudoroff, or pentose phosphate pathway for glycolytic carbon metabolism. To determine which of these pathways is used by intracellular S. flexneri, mutants were constructed and tested in a plaque assay for the ability to invade, replicate intracellularly, and spread to adjacent epithelial cells. Mutants blocked in the Embden-Meyerhof-Parnas pathway (pfkAB and pykAF mutants) invaded the cells but formed very small plaques. Loss of the Entner-Doudoroff pathway gene eda resulted in small plaques, but the double eda edd mutant formed normal-size plaques. This suggested that the plaque defect of the eda mutant was due to buildup of the toxic intermediate 2-keto-3-deoxy-6-phosphogluconic acid rather than a specific requirement for this pathway. Loss of the pentose phosphate pathway had no effect on plaque formation, indicating that it is not critical for intracellular S. flexneri. Supplementation of the epithelial cell culture medium with pyruvate allowed the glycolysis mutants to form larger plaques than those observed with unsupplemented medium, consistent with data from phenotypic microarrays (Biolog) indicating that pyruvate metabolism was not disrupted in these mutants. Interestingly, the wild-type S. flexneri also formed larger plaques in the presence of supplemental pyruvate or glucose, with pyruvate yielding the largest plaques. Analysis of the metabolites in the cultured cells showed increased intracellular levels of the added compound. Pyruvate increased the growth rate of S. flexneri in vitro, suggesting that it may be a preferred carbon source inside host cells.
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Pathogenesis of human enterovirulent bacteria: lessons from cultured, fully differentiated human colon cancer cell lines. Microbiol Mol Biol Rev 2014; 77:380-439. [PMID: 24006470 DOI: 10.1128/mmbr.00064-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hosts are protected from attack by potentially harmful enteric microorganisms, viruses, and parasites by the polarized fully differentiated epithelial cells that make up the epithelium, providing a physical and functional barrier. Enterovirulent bacteria interact with the epithelial polarized cells lining the intestinal barrier, and some invade the cells. A better understanding of the cross talk between enterovirulent bacteria and the polarized intestinal cells has resulted in the identification of essential enterovirulent bacterial structures and virulence gene products playing pivotal roles in pathogenesis. Cultured animal cell lines and cultured human nonintestinal, undifferentiated epithelial cells have been extensively used for understanding the mechanisms by which some human enterovirulent bacteria induce intestinal disorders. Human colon carcinoma cell lines which are able to express in culture the functional and structural characteristics of mature enterocytes and goblet cells have been established, mimicking structurally and functionally an intestinal epithelial barrier. Moreover, Caco-2-derived M-like cells have been established, mimicking the bacterial capture property of M cells of Peyer's patches. This review intends to analyze the cellular and molecular mechanisms of pathogenesis of human enterovirulent bacteria observed in infected cultured human colon carcinoma enterocyte-like HT-29 subpopulations, enterocyte-like Caco-2 and clone cells, the colonic T84 cell line, HT-29 mucus-secreting cell subpopulations, and Caco-2-derived M-like cells, including cell association, cell entry, intracellular lifestyle, structural lesions at the brush border, functional lesions in enterocytes and goblet cells, functional and structural lesions at the junctional domain, and host cellular defense responses.
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You L, Zhang B, Tang YJ. Application of stable isotope-assisted metabolomics for cell metabolism studies. Metabolites 2014; 4:142-65. [PMID: 24957020 PMCID: PMC4101500 DOI: 10.3390/metabo4020142] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 01/28/2023] Open
Abstract
The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to resolve overlapping peaks and background noises; and (5) data analysis methods and databases to decipher isotopic clusters over a broad m/z range (mass-to-charge ratio). This paper overviews mass spectrometry based techniques for precise determination of metabolites and their isotopologues. It also discusses applications of isotopic approaches to track substrate utilization, identify unknown metabolites and their chemical formulas, measure metabolite concentrations, determine putative metabolic pathways, and investigate microbial community populations and their carbon assimilation patterns. In addition, 13C-metabolite fingerprinting and metabolic models can be integrated to quantify carbon fluxes (enzyme reaction rates). The fluxome, in combination with other "omics" analyses, may give systems-level insights into regulatory mechanisms underlying gene functions. More importantly, 13C-tracer experiments significantly improve the potential of low-resolution gas chromatography-mass spectrometry (GC-MS) for broad-scope metabolism studies. We foresee the isotope-assisted metabolomics to be an indispensable tool in industrial biotechnology, environmental microbiology, and medical research.
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Affiliation(s)
- Le You
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA.
| | - Baichen Zhang
- Plant Metabolomics Group, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, CAS, Shanghai 20032, China.
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA.
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Lamichhane-Khadka R, Benoit SL, Maier SE, Maier RJ. A link between gut community metabolism and pathogenesis: molecular hydrogen-stimulated glucarate catabolism aids Salmonella virulence. Open Biol 2013; 3:130146. [PMID: 24307595 PMCID: PMC3877842 DOI: 10.1098/rsob.130146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Glucarate, an oxidized product of glucose, is a major serum organic acid in humans. Still, its role as a carbon source for a pathogen colonizing hosts has not been studied. We detected high-level expression of a potential glucarate permease encoding gene gudT when Salmonella enterica serovar Typhimurium are exposed to hydrogen gas (H2), a gaseous by-product of gut commensal metabolism. A gudT strain of Salmonella is deficient in glucarate-dependent growth, however, it can still use other monosaccharides, such as glucose or galactose. Complementation of the gudT mutant with a plasmid harbouring gudT restored glucarate-dependent growth to wild-type (WT) levels. The gudT mutant exhibits attenuated virulence: the mean time of death for mice inoculated with WT strain was 2 days earlier than for mice inoculated with the gudT strain. At 4 days postinoculation, liver and spleen homogenates from mice inoculated with a gudT strain contained significantly fewer viable Salmonella than homogenates from animals inoculated with the parent. The parent strain grew well H2-dependently in a minimal medium with amino acids and glucarate provided as the sole carbon sources, whereas the gudT strain achieved approximately 30% of the parent strain's yield. Glucarate-mediated growth of a mutant strain unable to produce H2 was stimulated by H2 addition, presumably owing to the positive transcriptional response to H2. Gut microbiota-produced molecular hydrogen apparently signals Salmonella to catabolize an alternative carbon source available in the host. Our results link a gut microbiome-produced diffusible metabolite to augmenting bacterial pathogenesis.
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Beste D, Nöh K, Niedenführ S, Mendum T, Hawkins N, Ward J, Beale M, Wiechert W, McFadden J. 13C-flux spectral analysis of host-pathogen metabolism reveals a mixed diet for intracellular Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2013; 20:1012-21. [PMID: 23911587 PMCID: PMC3752972 DOI: 10.1016/j.chembiol.2013.06.012] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/25/2013] [Accepted: 06/26/2013] [Indexed: 11/19/2022]
Abstract
Whereas intracellular carbon metabolism has emerged as an attractive drug target, the carbon sources of intracellularly replicating pathogens, such as the tuberculosis bacillus Mycobacterium tuberculosis, which causes long-term infections in one-third of the world’s population, remain mostly unknown. We used a systems-based approach—13C-flux spectral analysis (FSA) complemented with manual analysis—to measure the metabolic interaction between M. tuberculosis and its macrophage host cell. 13C-FSA analysis of experimental data showed that M. tuberculosis obtains a mixture of amino acids, C1 and C2 substrates from its host cell. We experimentally confirmed that the C1 substrate was derived from CO2. 13C labeling experiments performed on a phosphoenolpyruvate carboxykinase mutant revealed that intracellular M. tuberculosis has access to glycolytic C3 substrates. These findings provide constraints for developing novel chemotherapeutics. The intracellular metabolism of Mycobacterium tuberculosis was directly measured A tool for analyzing metabolic interactions between host and pathogen was developed Amino acids C1, C2, and C3 are intracellular substrates for M. tuberculosis CO2 was identified as an intracellular carbon source for M. tuberculosis
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Affiliation(s)
- Dany J.V. Beste
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Katharina Nöh
- Forschungszentrum Jülich, GmbH, IBG-1, Biotechnology and JARA-HPC, 52428 Jülich, Germany
| | - Sebastian Niedenführ
- Forschungszentrum Jülich, GmbH, IBG-1, Biotechnology and JARA-HPC, 52428 Jülich, Germany
| | - Tom A. Mendum
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nathaniel D. Hawkins
- National Centre for Plant and Microbial Metabolomics, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Jane L. Ward
- National Centre for Plant and Microbial Metabolomics, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Michael H. Beale
- National Centre for Plant and Microbial Metabolomics, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Wolfgang Wiechert
- Forschungszentrum Jülich, GmbH, IBG-1, Biotechnology and JARA-HPC, 52428 Jülich, Germany
| | - Johnjoe McFadden
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- Corresponding author
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Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. MOLECULAR BIOSYSTEMS 2013; 9:1522-34. [PMID: 23559334 PMCID: PMC3665296 DOI: 10.1039/c3mb25598k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative pathogen that uses complex mechanisms to invade and proliferate within mammalian host cells. To investigate possible contributions of metabolic processes to virulence in S. Typhimurium grown under conditions known to induce expression of virulence genes, we used a metabolomics-driven systems biology approach coupled with genome-scale modeling. First, we identified distinct metabolite profiles associated with bacteria grown in either rich or virulence-inducing media and report the most comprehensive coverage of the S. Typhimurium metabolome to date. Second, we applied an omics-informed genome-scale modeling analysis of the functional consequences of adaptive alterations in S. Typhimurium metabolism during growth under our conditions. Modeling efforts highlighted a decreased cellular capability to both produce and utilize intracellular amino acids during stationary phase culture in virulence conditions, despite significant abundance increases for these molecules as observed by our metabolomics measurements. Furthermore, analyses of omics data in the context of the metabolic model indicated rewiring of the metabolic network to support pathways associated with virulence. For example, cellular concentrations of polyamines were perturbed, as well as the predicted capacity for secretion and uptake.
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Affiliation(s)
- Young-Mo Kim
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Brian J. Schmidt
- Department of Bioengineering, University of California at San Diego, San Diego, CA 92093
| | - Afshan S. Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239
| | | | - Brooke L. Deatherage Kaiser
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Heather M. Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Hugh D. Mitchell
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California at San Diego, San Diego, CA 92093
| | - Jason E. McDermott
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239
| | - Richard D. Smith
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | | | - Charles Ansong
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Daniel R. Hyduke
- Department of Bioengineering, University of California at San Diego, San Diego, CA 92093
| | - Thomas O. Metz
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Joshua N. Adkins
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
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Growth media simulating ileal and colonic environments affect the intracellular proteome and carbon fluxes of enterohemorrhagic Escherichia coli O157:H7 strain EDL933. Appl Environ Microbiol 2013; 79:3703-15. [PMID: 23563955 DOI: 10.1128/aem.00062-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the intracellular proteome of Escherichia coli O157:H7 strain EDL933 was analyzed by two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) spectrometry after growth in simulated ileal environment media (SIEM) and simulated colonic environment media (SCEM) under aerobic and microaerobic conditions. Differentially expressed intracellular proteins were identified and allocated to functional protein groups. Moreover, metabolic fluxes were analyzed by isotopologue profiling with [U-(13)C(6)]glucose as a tracer. The results of this study show that EDL933 responds with differential expression of a complex network of proteins and metabolic pathways, reflecting the high metabolic adaptability of the strain. Growth in SIEM and SCEM is obviously facilitated by the upregulation of nucleotide biosynthesis pathway proteins and could be impaired by exposition to 50 µM 6-mercaptopurine under aerobic conditions. Notably, various stress and virulence factors, including Shiga toxin, were expressed without having contact with a human host.
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Abstract
Metabolic pathways and fluxes can be analyzed under in vivo conditions by incorporation experiments using general (13)C-labeled precursors. On the basis of the isotopologue compositions in amino acids or other metabolites, the incorporation rates of the supplied precursors and the pathways of their utilization can be studied in considerable detail. In this chapter, the method of isotopologue profiling is illustrated with recent work on the metabolism of intracellular living Legionella pneumophila.
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Gillmaier N, Götz A, Schulz A, Eisenreich W, Goebel W. Metabolic responses of primary and transformed cells to intracellular Listeria monocytogenes. PLoS One 2012; 7:e52378. [PMID: 23285016 PMCID: PMC3528701 DOI: 10.1371/journal.pone.0052378] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 11/12/2012] [Indexed: 02/08/2023] Open
Abstract
The metabolic response of host cells, in particular of primary mammalian cells, to bacterial infections is poorly understood. Here, we compare the carbon metabolism of primary mouse macrophages and of established J774A.1 cells upon Listeria monocytogenes infection using (13)C-labelled glucose or glutamine as carbon tracers. The (13)C-profiles of protein-derived amino acids from labelled host cells and intracellular L. monocytogenes identified active metabolic pathways in the different cell types. In the primary cells, infection with live L. monocytogenes increased glycolytic activity and enhanced flux of pyruvate into the TCA cycle via pyruvate dehydrogenase and pyruvate carboxylase, while in J774A.1 cells the already high glycolytic and glutaminolytic activities hardly changed upon infection. The carbon metabolism of intracellular L. monocytogenes was similar in both host cells. Taken together, the data suggest that efficient listerial replication in the cytosol of the host cells mainly depends on the glycolytic activity of the hosts.
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Affiliation(s)
- Nadine Gillmaier
- Lehrstuhl für Biochemie, Technische Universität München, Garching, Germany
| | - Andreas Götz
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität München, München, Germany
| | - Anette Schulz
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Werner Goebel
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität München, München, Germany
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Tang JKH, You L, Blankenship RE, Tang YJ. Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints. J R Soc Interface 2012; 9:2767-80. [PMID: 22896564 DOI: 10.1098/rsif.2012.0396] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
After feeding microbes with a defined (13)C substrate, unique isotopic patterns (isotopic fingerprints) can be formed in their metabolic products. Such labelling information not only can provide novel insights into functional pathways but also can determine absolute carbon fluxes through the metabolic network via metabolic modelling approaches. This technique has been used for finding pathways that may have been mis-annotated in the past, elucidating new enzyme functions, and investigating cell metabolisms in microbial communities. In this review paper, we summarize the applications of (13)C approaches to analyse novel cell metabolisms for the past 3 years. The isotopic fingerprints (defined as unique isotopomers useful for pathway identifications) have revealed the operations of the Entner-Doudoroff pathway, the reverse tricarboxylic acid cycle, new enzymes for biosynthesis of central metabolites, diverse respiration routes in phototrophic metabolism, co-metabolism of carbon nutrients and novel CO(2) fixation pathways. This review also discusses new isotopic methods to map carbon fluxes in global metabolisms, as well as potential factors influencing the metabolic flux quantification (e.g. metabolite channelling, the isotopic purity of (13)C substrates and the isotopic effect). Although (13)C labelling is not applicable to all biological systems (e.g. microbial communities), recent studies have shown that this method has a significant value in functional characterization of poorly understood micro-organisms, including species relevant for biotechnology and human health.
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Affiliation(s)
- Joseph Kuo-Hsiang Tang
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, USA
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Riganti C, Gazzano E, Polimeni M, Aldieri E, Ghigo D. The pentose phosphate pathway: an antioxidant defense and a crossroad in tumor cell fate. Free Radic Biol Med 2012; 53:421-36. [PMID: 22580150 DOI: 10.1016/j.freeradbiomed.2012.05.006] [Citation(s) in RCA: 298] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 04/14/2012] [Accepted: 05/03/2012] [Indexed: 01/10/2023]
Abstract
The pentose phosphate pathway, one of the main antioxidant cellular defense systems, has been related for a long time almost exclusively to its role as a provider of reducing power and ribose phosphate to the cell. In addition to this "traditional" correlation, in the past years multiple roles have emerged for this metabolic cascade, involving the cell cycle, apoptosis, differentiation, motility, angiogenesis, and the response to anti-tumor therapy. These findings make the pentose phosphate pathway a very interesting target in tumor cells. This review summarizes the latest discoveries relating the activity of the pentose phosphate pathway to various aspects of tumor metabolism, such as cell proliferation and death, tissue invasion, angiogenesis, and resistance to therapy, and discusses the possibility that drugs modulating the pathway could be used as potential tools in tumor therapy.
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Affiliation(s)
- Chiara Riganti
- Department of Genetics, Biology, and Biochemistry, University of Torino, Turin, Italy.
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Fuchs TM, Eisenreich W, Heesemann J, Goebel W. Metabolic adaptation of human pathogenic and related nonpathogenic bacteria to extra- and intracellular habitats. FEMS Microbiol Rev 2012; 36:435-62. [DOI: 10.1111/j.1574-6976.2011.00301.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 07/21/2011] [Indexed: 01/02/2023] Open
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