201
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Schulz C, Hammerschmidt S. Exploitation of physiology and metabolomics to identify pneumococcal vaccine candidates. Expert Rev Vaccines 2014; 12:1061-75. [PMID: 24053399 DOI: 10.1586/14760584.2013.824708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is the etiologic agent of community-acquired pneumonia and invasive pneumococcal diseases such as septicemia and bacterial meningitis. The increasing antibiotic resistance and the suboptimal efficacy or limited serotype coverage of currently available vaccines urgently requires novel approaches in exploring new antimicrobials, therapeutic intervention strategies and vaccines. The current vaccine development strategies rely on the hypothesis that surface-exposed proteins, which are essential for pneumococcal virulence, are the most suitable candidates for future protein-based vaccines. Since virulence is closely linked with bacterial fitness, the potential of a pathogen to colonize and infect the host depends further on its physiology. This review summarizes the application of genome-wide techniques and their exploitation to decipher fundamental insights into bacterial factors associated with fitness, metabolism and virulence, leading to the discovery of vaccine candidates or antimicrobials.
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Affiliation(s)
- Christian Schulz
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Strasse 15a, D 17487 Greifswald, Germany
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202
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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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203
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Eisele NA, Ruby T, Jacobson A, Manzanillo PS, Cox JS, Lam L, Mukundan L, Chawla A, Monack DM. Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence. Cell Host Microbe 2014; 14:171-182. [PMID: 23954156 DOI: 10.1016/j.chom.2013.07.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/10/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
Host-adapted Salmonella strains are responsible for a number of disease manifestations in mammals, including an asymptomatic chronic infection in which bacteria survive within macrophages located in systemic sites. However, the host cell physiology and metabolic requirements supporting bacterial persistence are poorly understood. In a mouse model of long-term infection, we found that S. typhimurium preferentially associates with anti-inflammatory/M2 macrophages at later stages of infection. Further, PPARδ, a eukaryotic transcription factor involved in sustaining fatty acid metabolism, is upregulated in Salmonella-infected macrophages. PPARδ deficiency dramatically inhibits Salmonella replication, which is linked to the metabolic state of macrophages and the level of intracellular glucose available to bacteria. Pharmacological activation of PPARδ increases glucose availability and enhances bacterial replication in macrophages and mice, while Salmonella fail to persist in Pparδ null mice. These data suggest that M2 macrophages represent a unique niche for long-term intracellular bacterial survival and link the PPARδ-regulated metabolic state of the host cell to persistent bacterial infection.
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Affiliation(s)
- Nicholas A Eisele
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Ruby
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amanda Jacobson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paolo S Manzanillo
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense. University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeffery S Cox
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense. University of California San Francisco, San Francisco, CA 94143, USA
| | - Lilian Lam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lata Mukundan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ajay Chawla
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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204
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Abstract
The nutrition of intracellular Mycobacterium tuberculosis is particularly experimentally intractable. In this issue of Chemistry and Biology, using 13C labeling with a new method of data analysis, Beste and colleagues provide direct evidence for the nutrients and pathways used by this ancient enemy of humanity.
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Affiliation(s)
- Natalie J Garton
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester LE1 9HN, UK
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205
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Omsland A, Sixt BS, Horn M, Hackstadt T. Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities. FEMS Microbiol Rev 2014; 38:779-801. [PMID: 24484402 DOI: 10.1111/1574-6976.12059] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/08/2014] [Accepted: 01/13/2014] [Indexed: 01/07/2023] Open
Abstract
Chlamydiae are a group of obligate intracellular bacteria comprising important human and animal pathogens as well as symbionts of ubiquitous protists. They are characterized by a developmental cycle including two main morphologically and physiologically distinct stages, the replicating reticulate body and the infectious nondividing elementary body. In this review, we reconstruct the history of studies that have led to our current perception of chlamydial physiology, focusing on their energy and central carbon metabolism. We then compare the metabolic capabilities of pathogenic and environmental chlamydiae highlighting interspecies variability among the metabolically more flexible environmental strains. We discuss recent findings suggesting that chlamydiae may not live as energy parasites throughout the developmental cycle and that elementary bodies are not metabolically inert but exhibit metabolic activity under appropriate axenic conditions. The observed host-free metabolic activity of elementary bodies may reflect adequate recapitulation of the intracellular environment, but there is evidence that this activity is biologically relevant and required for extracellular survival and maintenance of infectivity. The recent discoveries call for a reconsideration of chlamydial metabolism and future in-depth analyses to better understand how species- and stage-specific differences in chlamydial physiology may affect virulence, tissue tropism, and host adaptation.
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Affiliation(s)
- Anders Omsland
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, NIAID, NIH, Hamilton, MT, USA
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206
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Behrens S, Widder S, Mannala GK, Qing X, Madhugiri R, Kefer N, Mraheil MA, Rattei T, Hain T. Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs. PLoS One 2014; 9:e83979. [PMID: 24498259 PMCID: PMC3911899 DOI: 10.1371/journal.pone.0083979] [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: 05/14/2013] [Accepted: 11/08/2013] [Indexed: 11/19/2022] Open
Abstract
Listeria monocytogenes, a gram-positive pathogen, and causative agent of listeriosis, has become a widely used model organism for intracellular infections. Recent studies have identified small non-coding RNAs (sRNAs) as important factors for regulating gene expression and pathogenicity of L. monocytogenes. Increased speed and reduced costs of high throughput sequencing (HTS) techniques have made RNA sequencing (RNA-Seq) the state-of-the-art method to study bacterial transcriptomes. We created a large transcriptome dataset of L. monocytogenes containing a total of 21 million reads, using the SOLiD sequencing technology. The dataset contained cDNA sequences generated from L. monocytogenes RNA collected under intracellular and extracellular condition and additionally was size fractioned into three different size ranges from <40 nt, 40–150 nt and >150 nt. We report here, the identification of nine new sRNAs candidates of L. monocytogenes and a reevaluation of known sRNAs of L. monocytogenes EGD-e. Automatic comparison to known sRNAs revealed a high recovery rate of 55%, which was increased to 90% by manual revision of the data. Moreover, thorough classification of known sRNAs shed further light on their possible biological functions. Interestingly among the newly identified sRNA candidates are antisense RNAs (asRNAs) associated to the housekeeping genes purA, fumC and pgi and potentially their regulation, emphasizing the significance of sRNAs for metabolic adaptation in L. monocytogenes.
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Affiliation(s)
- Sebastian Behrens
- Department für Computational Systems Biology, Universität Wien, Wien, Austria
- Institute für Medizinische Mikrobiologie, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Stefanie Widder
- Department für Computational Systems Biology, Universität Wien, Wien, Austria
| | - Gopala Krishna Mannala
- Institute für Medizinische Mikrobiologie, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Xiaoxing Qing
- Institute für Medizinische Mikrobiologie, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Ramakanth Madhugiri
- Institute für Medizinische Virologie, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Nathalie Kefer
- febit biomed GmbH, Heidelberg, Germany
- Life Technologies GmbH, Darmstadt, Germany
| | - Mobarak Abu Mraheil
- Institute für Medizinische Mikrobiologie, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Thomas Rattei
- Department für Computational Systems Biology, Universität Wien, Wien, Austria
| | - Torsten Hain
- Institute für Medizinische Mikrobiologie, Justus-Liebig Universität Giessen, Giessen, Germany
- * E-mail:
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207
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Schatschneider S, Huber C, Neuweger H, Watt TF, Pühler A, Eisenreich W, Wittmann C, Niehaus K, Vorhölter FJ. Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner–Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis. ACTA ACUST UNITED AC 2014; 10:2663-76. [DOI: 10.1039/c4mb00198b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complex metabolic flux pattern ofX. campestris.
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Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie
- Center of Isotopologue Profiling
- Technische Universität München
- Garching, Germany
| | - Heiko Neuweger
- Computational Genomics
- Centrum für Biotechnology (CeBiTec)
- Universität Bielefeld
- Germany
| | - Tony Francis Watt
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
| | - Alfred Pühler
- Institut für Genomforschung und Systembiologie
- Centrum für Biotechnology (CeBiTec)
- Universität Bielefeld
- Bielefeld, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie
- Center of Isotopologue Profiling
- Technische Universität München
- Garching, Germany
| | - Christoph Wittmann
- Institut für Systembiotechnologie
- Universität des Saarlandes
- Saarbrücken, Germany
| | - Karsten Niehaus
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
- Institut für Genomforschung und Systembiologie
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208
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Pendini NR, Yap MY, Traore DAK, Polyak SW, Cowieson NP, Abell A, Booker GW, Wallace JC, Wilce JA, Wilce MCJ. Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Protein Sci 2013; 22:762-73. [PMID: 23559560 DOI: 10.1002/pro.2262] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 11/06/2022]
Abstract
The essential metabolic enzyme biotin protein ligase (BPL) is a potential target for the development of new antibiotics required to combat drug-resistant pathogens. Staphylococcus aureus BPL (SaBPL) is a bifunctional protein, possessing both biotin ligase and transcription repressor activities. This positions BPL as a key regulator of several important metabolic pathways. Here, we report the structural analysis of both holo- and apo-forms of SaBPL using X-ray crystallography. We also present small-angle X-ray scattering data of SaBPL in complex with its biotin-carboxyl carrier protein substrate as well as the SaBPL:DNA complex that underlies repression. This has revealed the molecular basis of ligand (biotinyl-5'-AMP) binding and conformational changes associated with catalysis and repressor function. These data provide new information to better understand the bifunctional activities of SaBPL and to inform future strategies for antibiotic discovery.
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Affiliation(s)
- Nicole R Pendini
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
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209
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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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210
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Wiechert W, Nöh K. Isotopically non-stationary metabolic flux analysis: complex yet highly informative. Curr Opin Biotechnol 2013; 24:979-86. [DOI: 10.1016/j.copbio.2013.03.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 12/16/2022]
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211
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Liebeke M, Lalk M. Staphylococcus aureus metabolic response to changing environmental conditions - a metabolomics perspective. Int J Med Microbiol 2013; 304:222-9. [PMID: 24439195 DOI: 10.1016/j.ijmm.2013.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/30/2013] [Accepted: 11/25/2013] [Indexed: 01/16/2023] Open
Abstract
Microorganisms preserve their metabolic function against a wide range of external perturbations including biotic or abiotic factors by utilizing cellular adaptations to maintain cell homeostasis. Functional genomics aims to detect such adaptive alterations on the level of transcriptome, proteome and metabolome to understand system wide changes and to identify interactions between the different levels of biochemical organization. Microbial metabolomics measures metabolites, the direct biochemical response to the environment, and is pivotal to the understanding of the variability and dynamics of bacterial cell metabolism. Metabolomics can measure many different types of compounds including primary metabolites, secondary metabolites, second messengers, quorum sensing compounds and others, which all contribute to the complex bacterial response to an environmental change. Recent data confirmed that many metabolic processes in pathogenic bacteria are linked to virulence and invasive capabilities. Deciphering bacterial metabolism in response to specific environmental conditions and in specific genetic backgrounds will help map the complex network between the metabolome and the other "-omes". Here, we will review a selection of case studies for the pathogenic Gram-positive bacterium Staphylococcus aureus and summarize the current state of metabolomics literature covering staphylococci metabolism under different physiological states.
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Affiliation(s)
- Manuel Liebeke
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University of Greifswald, 17487 Greifswald, Germany
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212
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Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms. ISME JOURNAL 2013; 8:908-24. [PMID: 24225886 DOI: 10.1038/ismej.2013.201] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 09/21/2013] [Accepted: 10/08/2013] [Indexed: 12/18/2022]
Abstract
An unusual symbiosis, first observed at ~3000 m depth in the Monterey Submarine Canyon, involves gutless marine polychaetes of the genus Osedax and intracellular endosymbionts belonging to the order Oceanospirillales. Ecologically, these worms and their microbial symbionts have a substantial role in the cycling of carbon from deep-sea whale fall carcasses. Microheterogeneity exists among the Osedax symbionts examined so far, and in the present study the genomes of the two dominant symbionts, Rs1 and Rs2, were sequenced. The genomes revealed heterotrophic versatility in carbon, phosphate and iron uptake, strategies for intracellular survival, evidence for an independent existence, and numerous potential virulence capabilities. The presence of specific permeases and peptidases (of glycine, proline and hydroxyproline), and numerous peptide transporters, suggests the use of degraded proteins, likely originating from collagenous bone matter, by the Osedax symbionts. (13)C tracer experiments confirmed the assimilation of glycine/proline, as well as monosaccharides, by Osedax. The Rs1 and Rs2 symbionts are genomically distinct in carbon and sulfur metabolism, respiration, and cell wall composition, among others. Differences between Rs1 and Rs2 and phylogenetic analysis of chemotaxis-related genes within individuals of symbiont Rs1 revealed the influence of the relative age of the whale fall environment and support possible local niche adaptation of 'free-living' lifestages. Future genomic examinations of other horizontally-propogated intracellular symbionts will likely enhance our understanding of the contribution of intraspecific symbiont diversity to the ecological diversification of the intact association, as well as the maintenance of host diversity.
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213
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Québatte M, Dick MS, Kaever V, Schmidt A, Dehio C. Dual input control: activation of theBartonella henselae VirB/D4 type IV secretion system by the stringent sigma factor RpoH1 and the BatR/BatS two-component system. Mol Microbiol 2013; 90:756-75. [DOI: 10.1111/mmi.12396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Maxime Québatte
- Focal Area Infection Biology, Biozentrum; University of Basel; Klingelbergstrasse 70 4056 Basel Switzerland
| | - Mathias S. Dick
- Focal Area Infection Biology, Biozentrum; University of Basel; Klingelbergstrasse 70 4056 Basel Switzerland
| | - Volkhard Kaever
- Research Core Unit for Mass Spectrometry - Metabolomics; Institute of Pharmacology; Hannover Medical School; Hannover Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum; University of Basel; Basel Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum; University of Basel; Klingelbergstrasse 70 4056 Basel Switzerland
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214
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Wink PL, Sanchez Quitian ZA, Rosado LA, Rodrigues VDS, Petersen GO, Lorenzini DM, Lipinski-Paes T, Saraiva Macedo Timmers LF, de Souza ON, Basso LA, Santos DS. Biochemical characterization of recombinant nucleoside hydrolase from Mycobacterium tuberculosis H37Rv. Arch Biochem Biophys 2013; 538:80-94. [DOI: 10.1016/j.abb.2013.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/13/2013] [Accepted: 08/17/2013] [Indexed: 11/25/2022]
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215
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Hammarlöf DL, Canals R, Hinton JCD. The FUN of identifying gene function in bacterial pathogens; insights from Salmonella functional genomics. Curr Opin Microbiol 2013; 16:643-51. [PMID: 24021902 DOI: 10.1016/j.mib.2013.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/12/2013] [Indexed: 02/01/2023]
Abstract
The availability of thousands of genome sequences of bacterial pathogens poses a particular challenge because each genome contains hundreds of genes of unknown function (FUN). How can we easily discover which FUN genes encode important virulence factors? One solution is to combine two different functional genomic approaches. First, transcriptomics identifies bacterial FUN genes that show differential expression during the process of mammalian infection. Second, global mutagenesis identifies individual FUN genes that the pathogen requires to cause disease. The intersection of these datasets can reveal a small set of candidate genes most likely to encode novel virulence attributes. We demonstrate this approach with the Salmonella infection model, and propose that a similar strategy could be used for other bacterial pathogens.
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Affiliation(s)
- Disa L Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
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216
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Watanabe S, Shimomura Y, Ubukata K, Kirikae T, Miyoshi-Akiyama T. Concomitant regulation of host tissue-destroying virulence factors and carbohydrate metabolism during invasive diseases induced by group g streptococci. J Infect Dis 2013; 208:1482-93. [PMID: 23901096 DOI: 10.1093/infdis/jit353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Streptococcus dysgalactiae subsp. equisimilis (SDSE) has Lancefield group G or C antigens. Recent epidemiological studies reveal that invasive SDSE infections have been increasing in Asia, Europe, and the United States. The mechanisms and key virulence factors by which SDSE causes invasive diseases are poorly understood. METHODS We analyzed the SDSE transcriptome in vivo during intraperitoneal infection in mice. We also compared the abundance of streptolysin S (SLS) and streptolysin O (SLO) production between clinically dominant stG6792 strains and other clinical isolates. RESULTS Microarray data suggest that SDSE degraded host tissue polysaccharides by secreting poly/oligosaccharide lyases and simultaneously used the Entner-Doudoroff pathway to metabolize acquired carbohydrates. A global negative virulence gene regulator CsrRS of SDSE modulated the expression of genes encoding SLS and enzymes that metabolize carbohydrates. Moreover, a csrS-deficient mutant induced severe systemic hemolysis in mice. The most frequently isolated stG6792 strains secreted abundant SLS and SLO rather than other SDSE emm types, indicating the potential relationship between production of SLS and SLO and poor outcomes. CONCLUSIONS Our findings suggest that the concomitant regulation of virulence factors that destroy host tissues and metabolic enzymes might play an important role in invasive diseases induced by SDSE.
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Affiliation(s)
- Shinya Watanabe
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine
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217
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Eisenreich W, Heesemann J, Rudel T, Goebel W. Metabolic host responses to infection by intracellular bacterial pathogens. Front Cell Infect Microbiol 2013; 3:24. [PMID: 23847769 PMCID: PMC3705551 DOI: 10.3389/fcimb.2013.00024] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/11/2013] [Indexed: 12/12/2022] Open
Abstract
The interaction of bacterial pathogens with mammalian hosts leads to a variety of physiological responses of the interacting partners aimed at an adaptation to the new situation. These responses include multiple metabolic changes in the affected host cells which are most obvious when the pathogen replicates within host cells as in case of intracellular bacterial pathogens. While the pathogen tries to deprive nutrients from the host cell, the host cell in return takes various metabolic countermeasures against the nutrient theft. During this conflicting interaction, the pathogen triggers metabolic host cell responses by means of common cell envelope components and specific virulence-associated factors. These host reactions generally promote replication of the pathogen. There is growing evidence that pathogen-specific factors may interfere in different ways with the complex regulatory network that controls the carbon and nitrogen metabolism of mammalian cells. The host cell defense answers include general metabolic reactions, like the generation of oxygen- and/or nitrogen-reactive species, and more specific measures aimed to prevent access to essential nutrients for the respective pathogen. Accurate results on metabolic host cell responses are often hampered by the use of cancer cell lines that already exhibit various de-regulated reactions in the primary carbon metabolism. Hence, there is an urgent need for cellular models that more closely reflect the in vivo infection conditions. The exact knowledge of the metabolic host cell responses may provide new interesting concepts for antibacterial therapies.
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Affiliation(s)
- Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Technische Universität München Garching, Germany
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218
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Ahmed Z, Zeeshan S, Huber C, Hensel M, Schomburg D, Münch R, Eisenreich W, Dandekar T. Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinformatics 2013; 14:218. [PMID: 23837681 PMCID: PMC3720290 DOI: 10.1186/1471-2105-14-218] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 06/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. RESULTS The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. CONCLUSIONS The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Saman Zeeshan
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie, Technische Universität München, München, Germany
| | - Michael Hensel
- Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technical University Braunschweig, Braunschweig, Germany
| | - Richard Münch
- Institute for Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | | | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- EMBL, Structural and Computational Biology Unit, Heidelberg, Germany
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219
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Hayden JD, Brown LR, Gunawardena HP, Perkowski EF, Chen X, Braunstein M. Reversible acetylation regulates acetate and propionate metabolism in Mycobacterium smegmatis. MICROBIOLOGY-SGM 2013; 159:1986-1999. [PMID: 23813678 DOI: 10.1099/mic.0.068585-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Carbon metabolic pathways are important to the pathogenesis of Mycobacterium tuberculosis, the causative agent of tuberculosis. However, extremely little is known about metabolic regulation in mycobacteria. There is growing evidence for lysine acetylation being a mechanism of regulating bacterial metabolism. Lysine acetylation is a post-translational modification in which an acetyl group is covalently attached to the side chain of a lysine residue. This modification is mediated by acetyltransferases, which add acetyl groups, and deacetylases, which remove the acetyl groups. Here we set out to test whether lysine acetylation and deacetylation impact acetate metabolism in the model mycobacteria Mycobacterium smegmatis, which possesses 25 candidate acetyltransferases and 3 putative lysine deacetylases. Using mutants lacking predicted acetyltransferases and deacetylases we showed that acetate metabolism in M. smegmatis is regulated by reversible acetylation of acetyl-CoA synthetase (Ms-Acs) through the action of a single pair of enzymes: the acetyltransferase Ms-PatA and the sirtuin deacetylase Ms-SrtN. We also confirmed that the role of Ms-PatA in regulating Ms-Acs regulation depends on cAMP binding. We additionally demonstrated a role for Ms-Acs, Ms-PatA and Ms-SrtN in regulating the metabolism of propionate in M. smegmatis. Finally, along with Ms-Acs, we identified a candidate propionyl-CoA synthetase, Ms5404, as acetylated in whole-cell lysates. This work lays the foundation for studying the regulatory circuit of acetylation and deacetylation in the cellular context of mycobacteria.
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Affiliation(s)
- Jennifer D Hayden
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lanisha R Brown
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ellen F Perkowski
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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220
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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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221
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Shafeeq S, Kuipers OP, Kloosterman TG. The role of zinc in the interplay between pathogenic streptococci and their hosts. Mol Microbiol 2013; 88:1047-57. [DOI: 10.1111/mmi.12256] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2013] [Indexed: 12/26/2022]
Affiliation(s)
- Sulman Shafeeq
- Department of Molecular Genetics; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 7; 9747 AG; Groningen; the Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 7; 9747 AG; Groningen; the Netherlands
| | - Tomas G. Kloosterman
- Department of Molecular Genetics; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 7; 9747 AG; Groningen; the Netherlands
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222
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Minato Y, Fassio SR, Häse CC. Malonate inhibits virulence gene expression in Vibrio cholerae. PLoS One 2013; 8:e63336. [PMID: 23675480 PMCID: PMC3652848 DOI: 10.1371/journal.pone.0063336] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 04/01/2013] [Indexed: 01/07/2023] Open
Abstract
We previously found that inhibition of the TCA cycle, either through mutations or chemical inhibition, increased toxT transcription in Vibrio cholerae. In this study, we found that the addition of malonate, an inhibitor of succinate dehydrogenase (SDH), decreased toxT transcription in V. cholerae, an observation inconsistent with the previous pattern observed. Unlike another SDH inhibitor, 2-thenoyltrifluoroacetone (TTFA), which increased toxT transcription and slightly inhibited V. cholerae growth, malonate inhibited toxT transcription in both the wild-type strain and TCA cycle mutants, suggesting malonate-mediated inhibition of virulence gene expression is independent to TCA cycle activity. Addition of malonate also inhibited ctxB and tcpA expressions but did not affect aphA, aphB, tcpP and toxR expressions. Malonate inhibited cholera toxin (CT) production in both V. cholerae classical biotype strains O395N1 and CA401, and El Tor biotype strain, N16961. Consistent with previous reports, we confirmed that these strains of V. cholerae did not utilize malonate as a primary carbon source. However, we found that the addition of malonate to the growth medium stimulated V. cholerae growth. All together, these results suggest that metabolizing malonate as a nutrient source negatively affects virulence gene expression in V. cholerae.
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Affiliation(s)
- Yusuke Minato
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Sara R. Fassio
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Claudia C. Häse
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, United States of America
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223
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Lv Y, Yin K, Shao S, Wang Q, Zhang Y. Comparative proteomic analysis reveals new components of the PhoP regulon and highlights a role for PhoP in the regulation of genes encoding the F1F0 ATP synthase in Edwardsiella tarda. MICROBIOLOGY-SGM 2013; 159:1340-1351. [PMID: 23657683 DOI: 10.1099/mic.0.066803-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Edwardsiella tarda is an important cause of haemorrhagic septicaemia in fish and also of gastro- and extra-intestinal infections in humans. We have recently demonstrated that the PhoP-PhoQ two-component regulatory system plays important roles in both virulence and stress tolerance in E. tarda. In this study, the proteomes of the WT and phoP mutant strains were compared to define components of the PhoP regulon in E. tarda EIB202. Overall, 18 proteins whose expression levels exhibited a twofold or greater change were identified; 13 of these proteins were found to require the presence of PhoP for full expression, while five were expressed at a higher level in the phoP mutant background. Identified proteins represented diverse functional categories, including energy production, amino acid metabolism and oxidative stress defence. Quantitative real-time PCR analysis of the mRNA levels for the identified proteins confirmed the proteomics data. Interestingly, the β subunit of the F1F0 ATP synthase, playing an important role in growth and virulence of E. tarda, was listed as one of the proteins whose expression was greatly dependent on PhoP. The F1F0 ATP synthase was encoded in a gene cluster (atpIBEFHAGDC) and the nine genes were transcribed as an operon. PhoP positively regulated the transcription of the nine ATP synthase genes and exerted this effect through direct binding to the promoter of atpI. Overall, the results provide new insights into the PhoP regulon and unravel a novel role for PhoP in the regulation of the F1F0 ATP synthase.
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Affiliation(s)
- Yuanzhi Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kaiyu Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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224
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Steeb B, Claudi B, Burton NA, Tienz P, Schmidt A, Farhan H, Mazé A, Bumann D. Parallel exploitation of diverse host nutrients enhances Salmonella virulence. PLoS Pathog 2013; 9:e1003301. [PMID: 23633950 PMCID: PMC3636032 DOI: 10.1371/journal.ppat.1003301] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 02/26/2013] [Indexed: 12/20/2022] Open
Abstract
Pathogen access to host nutrients in infected tissues is fundamental for pathogen growth and virulence, disease progression, and infection control. However, our understanding of this crucial process is still rather limited because of experimental and conceptual challenges. Here, we used proteomics, microbial genetics, competitive infections, and computational approaches to obtain a comprehensive overview of Salmonella nutrition and growth in a mouse typhoid fever model. The data revealed that Salmonella accessed an unexpectedly diverse set of at least 31 different host nutrients in infected tissues but the individual nutrients were available in only scarce amounts. Salmonella adapted to this situation by expressing versatile catabolic pathways to simultaneously exploit multiple host nutrients. A genome-scale computational model of Salmonella in vivo metabolism based on these data was fully consistent with independent large-scale experimental data on Salmonella enzyme quantities, and correctly predicted 92% of 738 reported experimental mutant virulence phenotypes, suggesting that our analysis provided a comprehensive overview of host nutrient supply, Salmonella metabolism, and Salmonella growth during infection. Comparison of metabolic networks of other pathogens suggested that complex host/pathogen nutritional interfaces are a common feature underlying many infectious diseases.
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Affiliation(s)
- Benjamin Steeb
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Beatrice Claudi
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Neil A. Burton
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Petra Tienz
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Hesso Farhan
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Alain Mazé
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Dirk Bumann
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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225
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Ramond E, Gesbert G, Barel M, Charbit A. Proteins involved in Francisella tularensis survival and replication inside macrophages. Future Microbiol 2013; 7:1255-68. [PMID: 23075445 DOI: 10.2217/fmb.12.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Francisella tularensis, the etiological agent of tularemia, is a member of the γ-proteobacteria class of Gram-negative bacteria. This highly virulent bacterium can infect a large range of mammalian species and has been recognized as a human pathogen for a century. F. tularensis is able to survive in vitro in a variety of cell types. In vivo, the bacterium replicates mainly in infected macrophages, using the cytoplasmic compartment as a replicative niche. To successfully adapt to this stressful environment, F. tularensis must simultaneously: produce and regulate the expression of a series of dedicated virulence factors; adapt its metabolic needs to the nutritional context of the host cytosol; and control the innate immune cytosolic surveillance pathways to avoid premature cell death. We will focus here on the secretion or release of bacterial proteins in the host, as well as on the envelope proteins, involved in bacterial survival inside macrophages.
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Affiliation(s)
- Elodie Ramond
- Faculté de Médecine Necker, Université Paris Descartes, 156 Rue de Vaugirard, 75730 Paris, Cedex 15, France
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226
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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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227
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Zhang YJ, Rubin EJ. Feast or famine: the host-pathogen battle over amino acids. Cell Microbiol 2013; 15:1079-87. [PMID: 23521858 DOI: 10.1111/cmi.12140] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 01/28/2023]
Abstract
Intracellular bacterial pathogens often rely on their hosts for essential nutrients. Host cells, in turn, attempt to limit nutrient availability, using starvation as a mechanism of innate immunity. Here we discuss both host mechanisms of amino acid starvation and the diverse adaptations of pathogens to their nutrient-deprived environments. These processes provide both key insights into immune subversion and new targets for drug development.
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Affiliation(s)
- Yanjia J Zhang
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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228
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Abu Kwaik Y, Bumann D. Microbial quest for food in vivo: 'nutritional virulence' as an emerging paradigm. Cell Microbiol 2013; 15:882-90. [PMID: 23490329 DOI: 10.1111/cmi.12138] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/05/2013] [Accepted: 03/07/2013] [Indexed: 12/14/2022]
Abstract
Microbial access to host nutrients is a fundamental aspect of infectious diseases. Pathogens face complex dynamic nutritional host microenvironments that change with increasing inflammation and local hypoxia. Since the host can actively limit microbial access to nutrient supply, pathogens have evolved various metabolic adaptations to successfully exploit available host nutrients for proliferation. Recent studies have unraveled an emerging paradigm that we propose to designate as 'nutritional virulence'. This paradigm is based on specific virulence mechanisms that target major host biosynthetic and degradation pathways (proteasomes, autophagy and lysosomes) or nutrient-rich sources, such as glutathione, to enhance host supply of limiting nutrients, such as cysteine. Although Cys is the most limiting cellular amino acid, it is a metabolically favourable source of carbon and energy for various pathogens that are auxotrophic for Cys but utilize idiosyncratic nutritional virulence strategies to generate a gratuitous supply of host Cys. Therefore, proliferation of some intracellular pathogens is restricted by a host nutritional rheostat regulated by certain limiting amino acids, and pathogens have evolved idiosyncratic strategies to short circuit the host nutritional rheostat. Deciphering mechanisms of microbial 'nutritional virulence' and metabolism in vivo will facilitate identification of novel microbialand host targets for treatment and prevention of infectious diseases. Host-pathogen synchronization of amino acid auxotrophy indicates that this nutritional synchronization has been a major driving force in the evolution of many intracellular bacterial pathogens.
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Affiliation(s)
- Yousef Abu Kwaik
- Department of Microbiology and Immunology, College of Medicine, University of Louisville, Louisville, KY 40202, USA.
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229
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Weigoldt M, Meens J, Bange FC, Pich A, Gerlach GF, Goethe R. Metabolic adaptation of Mycobacterium avium subsp. paratuberculosis to the gut environment. Microbiology (Reading) 2013; 159:380-391. [DOI: 10.1099/mic.0.062737-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mathias Weigoldt
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Franz-Christoph Bange
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Medical School Hannover, Hannover, Germany
| | - Gerald F. Gerlach
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
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230
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Slayden RA, Jackson M, Zucker J, Ramirez MV, Dawson CC, Crew R, Sampson NS, Thomas ST, Jamshidi N, Sisk P, Caspi R, Crick DC, McNeil MR, Pavelka MS, Niederweis M, Siroy A, Dona V, McFadden J, Boshoff H, Lew JM. Updating and curating metabolic pathways of TB. Tuberculosis (Edinb) 2013; 93:47-59. [PMID: 23375378 DOI: 10.1016/j.tube.2012.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 11/25/2012] [Indexed: 01/08/2023]
Abstract
The sequencing of complete genomes has accelerated biomedical research by providing information about the overall coding capacity of bacterial chromosomes. The original TB annotation resulted in putative functional assignment of ∼60% of the genes to specific metabolic functions, however, the other 40% of the encoded ORFs where annotated as conserved hypothetical proteins, hypothetical proteins or encoding proteins of unknown function. The TB research community is now at the beginning of the next phases of post-genomics; namely reannotation and functional characterization by targeted experimentation. Arguably, this is the most significant time for basic microbiology in recent history. To foster basic TB research, the Tuberculosis Community Annotation Project (TBCAP) jamboree exercise began the reannotation effort by providing additional information for previous annotations, and refining and substantiating the functional assignment of ORFs and genes within metabolic pathways. The overall goal of the TBCAP 2012 exercise was to gather and compile various data types and use this information with oversight from the scientific community to provide additional information to support the functional annotations of encoding genes. Another objective of this effort was to standardize the publicly accessible Mycobacterium tuberculosis reference sequence and its annotation. The greatest benefit of functional annotation information of genome sequence is that it fuels TB research for drug discovery, diagnostics, vaccine development and epidemiology.
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231
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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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232
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Sun Y, O'Riordan MXD. Regulation of bacterial pathogenesis by intestinal short-chain Fatty acids. ADVANCES IN APPLIED MICROBIOLOGY 2013; 85:93-118. [PMID: 23942149 PMCID: PMC4029053 DOI: 10.1016/b978-0-12-407672-3.00003-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human gut microbiota is inextricably linked to health and disease. One important function of the commensal organisms living in the intestine is to provide colonization resistance against invading enteric pathogens. Because of the complex nature of the interaction between the microbiota and its host, multiple mechanisms likely contribute to resistance. In this review, we dissect the biological role of short-chain fatty acids (SCFA), which are fermentation end products of the intestinal microbiota, in host-pathogen interactions. SCFA exert an extensive influence on host physiology through nutritional, regulatory, and immunomodulatory functions and can also affect bacterial fitness as a form of acid stress. Moreover, SCFA act as a signal for virulence gene regulation in common enteric pathogens. Taken together, these studies highlight the importance of the chemical environment where the biology of the host, the microbiota, and the pathogen intersects, which provides a basis for designing effective infection prevention and control.
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Affiliation(s)
- Yvonne Sun
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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233
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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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Skvortsov TA, Azhikina TL. [Adaptive changes of Mycobacterium tuberculosis gene expression during the infectious process]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [PMID: 23189553 DOI: 10.1134/s1068162012040139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mycobacterium tuberculosis causes an infection in humans with clinical manifestations varying from asymptomatic carriage of bacteria to rapidly progressing tuberculosis. Infection outcomes depend on complex and still not fully understood interactions between the pathogenic bacteria and their host organism. Gene expression changes in response to host defense mechanisms are needed for M. tuberculosis survival and functioning. This review focuses on the analysis of dynamic changes in the M. tuberculosis transcriptome taking place during infection processes in host tissues. Presently available data on mycobacterial transcriptome changes obtained from different infection models are discussed. A major part of this review is devoted to the description of biochemical changes occurring in M. tuberculosis infection process, from the primary through latent infection to pathogen reactivation. At each stage of the infection, gene expression changes and induced bacterial metabolic variations are discussed.
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235
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Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Völker U, Dandekar T. Metabolic adaptation and protein complexes in prokaryotes. Metabolites 2012; 2:940-58. [PMID: 24957769 PMCID: PMC3901225 DOI: 10.3390/metabo2040940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 02/07/2023] Open
Abstract
Protein complexes are classified and have been charted in several large-scale screening studies in prokaryotes. These complexes are organized in a factory-like fashion to optimize protein production and metabolism. Central components are conserved between different prokaryotes; major complexes involve carbohydrate, amino acid, fatty acid and nucleotide metabolism. Metabolic adaptation changes protein complexes according to environmental conditions. Protein modification depends on specific modifying enzymes. Proteins such as trigger enzymes display condition-dependent adaptation to different functions by participating in several complexes. Several bacterial pathogens adapt rapidly to intracellular survival with concomitant changes in protein complexes in central metabolism and optimize utilization of their favorite available nutrient source. Regulation optimizes protein costs. Master regulators lead to up- and downregulation in specific subnetworks and all involved complexes. Long protein half-life and low level expression detaches protein levels from gene expression levels. However, under optimal growth conditions, metabolite fluxes through central carbohydrate pathways correlate well with gene expression. In a system-wide view, major metabolic changes lead to rapid adaptation of complexes and feedback or feedforward regulation. Finally, prokaryotic enzyme complexes are involved in crowding and substrate channeling. This depends on detailed structural interactions and is verified for specific effects by experiments and simulations.
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Affiliation(s)
- Beate Krüger
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Florian Prell
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Astrid Fieselmann
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Andres Moya
- Unidad Mixta de Investigación en Genómica y Salud CSISP-UVEG, University of València José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Straße 15a, 17487, Greifswald, Germany.
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
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Dandekar T, Fieselmann A, Majeed S, Ahmed Z. Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform 2012; 15:91-107. [PMID: 23142828 DOI: 10.1093/bib/bbs065] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metabolites and their pathways are central for adaptation and survival. Metabolic modeling elucidates in silico all the possible flux pathways (flux balance analysis, FBA) and predicts the actual fluxes under a given situation, further refinement of these models is possible by including experimental isotopologue data. In this review, we initially introduce the key theoretical concepts and different analysis steps in the modeling process before comparing flux calculation and metabolite analysis programs such as C13, BioOpt, COBRA toolbox, Metatool, efmtool, FiatFlux, ReMatch, VANTED, iMAT and YANA. Their respective strengths and limitations are discussed and compared to alternative software. While data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific changes are all possible, we highlight the considerations that need to be taken into account before deciding on a specific software. Current challenges in the field include the computation of large-scale networks (in elementary mode analysis), regulatory interactions and detailed kinetics, and these are discussed in the light of powerful new approaches.
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Affiliation(s)
- Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Wüerzburg, Am Hubland, 97074 Wuerzburg, Germany. Tel.: +49-931-318-4551; Fax: +49-931-318-4552;
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237
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Forrellad MA, Klepp LI, Gioffré A, Sabio y García J, Morbidoni HR, de la Paz Santangelo M, Cataldi AA, Bigi F. Virulence factors of the Mycobacterium tuberculosis complex. Virulence 2012; 4:3-66. [PMID: 23076359 PMCID: PMC3544749 DOI: 10.4161/viru.22329] [Citation(s) in RCA: 379] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) consists of closely related species that cause tuberculosis in both humans and animals. This illness, still today, remains to be one of the leading causes of morbidity and mortality throughout the world. The mycobacteria enter the host by air, and, once in the lungs, are phagocytated by macrophages. This may lead to the rapid elimination of the bacillus or to the triggering of an active tuberculosis infection. A large number of different virulence factors have evolved in MTBC members as a response to the host immune reaction. The aim of this review is to describe the bacterial genes/proteins that are essential for the virulence of MTBC species, and that have been demonstrated in an in vivo model of infection. Knowledge of MTBC virulence factors is essential for the development of new vaccines and drugs to help manage the disease toward an increasingly more tuberculosis-free world.
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238
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Functional γ-Aminobutyrate Shunt in Listeria monocytogenes: role in acid tolerance and succinate biosynthesis. Appl Environ Microbiol 2012; 79:74-80. [PMID: 23064337 DOI: 10.1128/aem.02184-12] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes, the causative agent of human listeriosis, is known for its ability to withstand severe environmental stresses. The glutamate decarboxylase (GAD) system is one of the principal systems utilized by the bacterium to cope with acid stress, a reaction that produces γ-aminobutyrate (GABA) from glutamate. Recently, we have shown that GABA can accumulate intracellularly under acidic conditions, even under conditions where no extracellular glutamate-GABA exchange is detectable. The GABA shunt, a pathway that metabolizes GABA to succinate, has been described for several other bacterial genera, and the present study sought to determine whether L. monocytogenes has this metabolic capacity, which, if present, could provide a possible route for succinate biosynthesis in L. monocytogenes. Using crude protein extracts from L. monocytogenes EGD-e, we show that this strain exhibits activity for the two main enzyme reactions in the GABA shunt, GABA aminotransferase (GABA-AT) and succinic semialdehyde dehydrogenase (SSDH). Two genes were identified as candidates for encoding these enzyme activities, argD (GABA-AT) and lmo0913 (SSDH). Crude protein extracts prepared from a mutant lacking a functional argD gene significantly reduced GABA-AT activity, while an lmo0913 mutant lost all detectable SSDH activity. The deletion of lmo0913 increased the acid tolerance of EGD-e and showed an increased accumulation of intracellular GABA, suggesting that this pathway plays a significant role in the survival of this pathogen under acidic conditions. This is the first report of such a pathway in the genus Listeria, which highlights an important link between metabolism and acid tolerance and also presents a possible compensatory pathway to partially overcome the incomplete tricarboxylic acid cycle of Listeria.
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239
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Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. PLoS Genet 2012; 8:e1002887. [PMID: 22969433 PMCID: PMC3435247 DOI: 10.1371/journal.pgen.1002887] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 06/24/2012] [Indexed: 12/12/2022] Open
Abstract
Intracellular bacterial pathogens are metabolically adapted to grow within mammalian cells. While these adaptations are fundamental to the ability to cause disease, we know little about the relationship between the pathogen's metabolism and virulence. Here we used an integrative Metabolic Analysis Tool that combines transcriptome data with genome-scale metabolic models to define the metabolic requirements of Listeria monocytogenes during infection. Twelve metabolic pathways were identified as differentially active during L. monocytogenes growth in macrophage cells. Intracellular replication requires de novo synthesis of histidine, arginine, purine, and branch chain amino acids (BCAAs), as well as catabolism of L-rhamnose and glycerol. The importance of each metabolic pathway during infection was confirmed by generation of gene knockout mutants in the respective pathways. Next, we investigated the association of these metabolic requirements in the regulation of L. monocytogenes virulence. Here we show that limiting BCAA concentrations, primarily isoleucine, results in robust induction of the master virulence activator gene, prfA, and the PrfA-regulated genes. This response was specific and required the nutrient responsive regulator CodY, which is known to bind isoleucine. Further analysis demonstrated that CodY is involved in prfA regulation, playing a role in prfA activation under limiting conditions of BCAAs. This study evidences an additional regulatory mechanism underlying L. monocytogenes virulence, placing CodY at the crossroads of metabolism and virulence. Intracellular bacterial pathogens have developed sophisticated mechanisms to invade and replicate within eukaryotic cells. For successful replication, pathogens have adapted metabolically to the intracellular niche. While this adaptation is fundamental to the ability to cause disease, we know little about pathogen's intracellular metabolism and its association with virulence. In this study we took a global approach that combines computational and experimental methods to decipher the intracellular metabolic requirements of the human bacterial pathogen Listeria monocytogenes. We identified 12 metabolic pathways to be differentially active during infection in comparison to growth in rich lab media. We validated the essentiality of the active pathways for L. monocytogenes intracellular replication. Pathways included: biosynthesis of histidine, arginine, purine, and branch chain amino acids (BCAAs), as well as the catabolism of L-rhamnose and glycerol. Next we analyzed whether the requirement for these nutrients associates with virulence. We found that limiting concentrations of BCAAs, primarily of isoleucine, results in robust induction of the bacterial virulence state, a response that is dependent on the isoleucine responsive regulator, CodY. CodY was responsible for the up-regulation of the major virulence regulator of L. monocytogenes, PrfA. This study supports the premise that pathogens metabolism and virulence are closely interlinked.
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240
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Abstract
Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “omics” platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology.
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Affiliation(s)
- Jane Tang
- Center for National Security and Intelligence, Noblis, Falls Church, Virginia, USA
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241
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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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Abstract
The analysis of the genomes of bacterial pathogens indicates that they have acquired their pathogenic capability by incorporating different genetic elements through horizontal gene transfer. The ancestors of virulent bacteria, as well as the origin of virulence determinants, lay most likely in the environmental microbiota. Studying the role that these determinants may have in non-clinical ecosystems is thus of value for understanding in detail the evolution and the ecology of bacterial pathogens. In this article, I propose that classical virulence determinants might be relevant for basic metabolic processes (for instance iron-uptake systems) or in modulating prey/predator relationships (toxins) in natural, non-infective ecosystems. The different role that horizontal gene transfer and mutation may have in the evolution of bacterial pathogens either for their speciation or in short-sighted evolution processes is also discussed.
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Affiliation(s)
- José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Darwin 3, Cantoblanco, 28049-Madrid, Spain.
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243
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Nutritional immunity: transition metals at the pathogen-host interface. Nat Rev Microbiol 2012; 10:525-37. [PMID: 22796883 DOI: 10.1038/nrmicro2836] [Citation(s) in RCA: 1050] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transition metals occupy an essential niche in biological systems. Their electrostatic properties stabilize substrates or reaction intermediates in the active sites of enzymes, and their heightened reactivity is harnessed for catalysis. However, this heightened activity also renders transition metals toxic at high concentrations. Bacteria, like all living organisms, must regulate their intracellular levels of these elements to satisfy their physiological needs while avoiding harm. It is therefore not surprising that the host capitalizes on both the essentiality and toxicity of transition metals to defend against bacterial invaders. This Review discusses established and emerging paradigms in nutrient metal homeostasis at the pathogen-host interface.
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244
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Vinuselvi P, Kim MK, Lee SK, Ghim CM. Rewiring carbon catabolite repression for microbial cell factory. BMB Rep 2012; 45:59-70. [PMID: 22360882 DOI: 10.5483/bmbrep.2012.45.2.59] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon catabolite repression (CCR) is a key regulatory system found in most microorganisms that ensures preferential utilization of energy-efficient carbon sources. CCR helps microorganisms obtain a proper balance between their metabolic capacity and the maximum sugar uptake capability. It also constrains the deregulated utilization of a preferred cognate substrate, enabling microorganisms to survive and dominate in natural environments. On the other side of the same coin lies the tenacious bottleneck in microbial production of bioproducts that employs a combination of carbon sources in varied proportion, such as lignocellulose-derived sugar mixtures. Preferential sugar uptake combined with the transcriptional and/or enzymatic exclusion of less preferred sugars turns out one of the major barriers in increasing the yield and productivity of fermentation process. Accumulation of the unused substrate also complicates the downstream processes used to extract the desired product. To overcome this difficulty and to develop tailor-made strains for specific metabolic engineering goals, quantitative and systemic understanding of the molecular interaction map behind CCR is a prerequisite. Here we comparatively review the universal and strain-specific features of CCR circuitry and discuss the recent efforts in developing synthetic cell factories devoid of CCR particularly for lignocellulose- based biorefinery.
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Affiliation(s)
- Parisutham Vinuselvi
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
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245
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Ketoglutarate transport protein KgtP is secreted through the type III secretion system and contributes to virulence in Xanthomonas oryzae pv. oryzae. Appl Environ Microbiol 2012; 78:5672-81. [PMID: 22685129 DOI: 10.1128/aem.07997-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The phytopathogenic prokaryote Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight (BB) of rice and utilizes a type III secretion system (T3SS) to deliver T3SS effectors into rice cells. In this report, we show that the ketoglutarate transport protein (KgtP) is secreted in an HpaB-independent manner through the T3SS of X. oryzae pv. oryzae PXO99(A) and localizes to the host cell membrane for α-ketoglutaric acid export. kgtP contained an imperfect PIP box (plant-inducible promoter) in the promoter region and was positively regulated by HrpX and HrpG. A kgtP deletion mutant was impaired in bacterial virulence and growth in planta; furthermore, the mutant showed reduced growth in minimal media containing α-ketoglutaric acid or sodium succinate as the sole carbon source. The reduced virulence and the deficiency in α-ketoglutaric acid utilization by the kgtP mutant were restored to wild-type levels by the presence of kgtP in trans. The expression of OsIDH, which is responsible for the synthesis of α-ketoglutaric acid in rice, was enhanced when KgtP was present in the pathogen. To our knowledge, this is the first report demonstrating that KgtP, which is regulated by HrpG and HrpX and secreted by the T3SS in Xanthomonas oryzae pv. oryzae, transports α-ketoglutaric acid when the pathogen infects rice.
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246
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Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One 2012; 7:e37919. [PMID: 22675498 PMCID: PMC3366996 DOI: 10.1371/journal.pone.0037919] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/30/2012] [Indexed: 11/18/2022] Open
Abstract
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.
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Affiliation(s)
- Bo Liu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
| | - Lina L. Faller
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Niels Klitgord
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Varun Mazumdar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Mohammad Ghodsi
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
| | - Daniel D. Sommer
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Theodore R. Gibbons
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, United States of America
| | - Todd J. Treangen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- The McKusick-Nathans Institute for Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yi-Chien Chang
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Shan Li
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - O. Colin Stine
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hatice Hasturk
- The Forysth Institute, Department of Periodontology, Cambridge, Massachusetts, United States of America
| | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Children’s Informatics Program, Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, United States of America
| | - Salomon Amar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Center for Anti-Inflammatory Therapeutics; Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
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247
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FdhTU-modulated formate dehydrogenase expression and electron donor availability enhance recovery of Campylobacter jejuni following host cell infection. J Bacteriol 2012; 194:3803-13. [PMID: 22636777 DOI: 10.1128/jb.06665-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Campylobacter jejuni is a food-borne bacterial pathogen that colonizes the intestinal tract and causes severe gastroenteritis. Interaction with host epithelial cells is thought to enhance severity of disease, and the ability of C. jejuni to modulate its metabolism in different in vivo and environmental niches contributes to its success as a pathogen. A C. jejuni operon comprising two genes that we designated fdhT (CJJ81176_1492) and fdhU (CJJ81176_1493) is conserved in many bacterial species. Deletion of fdhT or fdhU in C. jejuni resulted in apparent defects in adherence and/or invasion of Caco-2 epithelial cells when assessed by CFU enumeration on standard Mueller-Hinton agar. However, fluorescence microscopy indicated that each mutant invaded cells at wild-type levels, instead suggesting roles for FdhTU in either intracellular survival or postinvasion recovery. The loss of fdhU caused reduced mRNA levels of formate dehydrogenase (FDH) genes and a severe defect in FDH activity. Cell infection phenotypes of a mutant deleted for the FdhA subunit of FDH and an ΔfdhU ΔfdhA double mutant were similar to those of a ΔfdhU mutant, which likewise suggested that FdhU and FdhA function in the same pathway. Cell infection assays followed by CFU enumeration on plates supplemented with sodium sulfite abolished the ΔfdhU and ΔfdhA mutant defects and resulted in significantly enhanced recovery of all strains, including wild type, at the invasion and intracellular survival time points. Collectively, our data indicate that FdhTU and FDH are required for optimal recovery following cell infection and suggest that C. jejuni alters its metabolic potential in the intracellular environment.
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248
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Chai LC, Kong BH, Elemfareji OI, Thong KL. Variable carbon catabolism among Salmonella enterica serovar Typhi isolates. PLoS One 2012; 7:e36201. [PMID: 22662115 PMCID: PMC3360705 DOI: 10.1371/journal.pone.0036201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/03/2012] [Indexed: 12/22/2022] Open
Abstract
Background Salmonella enterica serovar Typhi (S. Typhi) is strictly a human intracellular pathogen. It causes acute systemic (typhoid fever) and chronic infections that result in long-term asymptomatic human carriage. S. Typhi displays diverse disease manifestations in human infection and exhibits high clonality. The principal factors underlying the unique lifestyle of S. Typhi in its human host during acute and chronic infections remain largely unknown and are therefore the main objective of this study. Methodology/Principal Findings To obtain insight into the intracellular lifestyle of S. Typhi, a high-throughput phenotypic microarray was employed to characterise the catabolic capacity of 190 carbon sources in S. Typhi strains. The success of this study lies in the carefully selected library of S. Typhi strains, including strains from two geographically distinct areas oftyphoid endemicity, an asymptomatic human carrier, clinical stools and blood samples and sewage-contaminated rivers. An extremely low carbon catabolic capacity (27% of 190 carbon substrates) was observed among the strains. The carbon catabolic profiles appeared to suggest that S. Typhi strains survived well on carbon subtrates that are found abundantly in the human body but not in others. The strains could not utilise plant-associated carbon substrates. In addition, α-glycerolphosphate, glycerol, L-serine, pyruvate and lactate served as better carbon sources to monosaccharides in the S. Typhi strains tested. Conclusion The carbon catabolic profiles suggest that S. Typhi could survive and persist well in the nutrient depleted metabolic niches in the human host but not in the environment outside of the host. These findings serve as caveats for future studies to understand how carbon catabolism relates to the pathogenesis and transmission of this pathogen.
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Affiliation(s)
- Lay Ching Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Boon Hong Kong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Omar Ismail Elemfareji
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Dandekar T, Astrid F, Jasmin P, Hensel M. Salmonella enterica: a surprisingly well-adapted intracellular lifestyle. Front Microbiol 2012; 3:164. [PMID: 22563326 PMCID: PMC3342586 DOI: 10.3389/fmicb.2012.00164] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/12/2012] [Indexed: 11/15/2022] Open
Abstract
The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole (SCV) in host cells. We summarize latest results on metabolic requirements for Salmonella during infection. This includes intracellular phenotypes of mutant strains based on metabolic modeling and experimental tests, isotopolog profiling using 13C-compounds in intracellular Salmonella, and complementation of metabolic defects for attenuated mutant strains towards a comprehensive understanding of the metabolic requirements of the intracellular lifestyle of Salmonella. Helpful for this are also genomic comparisons. We outline further recent studies and which analyses of intracellular phenotypes and improved metabolic simulations were done and comment on technical required steps as well as progress involved in the iterative refinement of metabolic flux models, analyses of mutant phenotypes, and isotopolog analyses. Salmonella lifestyle is well-adapted to the SCV and its specific metabolic requirements. Salmonella metabolism adapts rapidly to SCV conditions, the metabolic generalist Salmonella is quite successful in host infection.
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Affiliation(s)
- Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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Hertzén E, Johansson L, Kansal R, Hecht A, Dahesh S, Janos M, Nizet V, Kotb M, Norrby-Teglund A. Intracellular Streptococcus pyogenes in human macrophages display an altered gene expression profile. PLoS One 2012; 7:e35218. [PMID: 22511985 PMCID: PMC3325220 DOI: 10.1371/journal.pone.0035218] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/10/2012] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pyogenes is an important human pathogen, which has recently gained recognition as an intracellular microorganism during the course of severe invasive infections such as necrotizing fasciitis. Although the surface anchored M protein has been identified as a pivotal factor affecting phagosomal maturation and S. pyogenes survival within macrophages, the overall transcriptional profile required for the pathogen to adapt and persist intracellularly is as of yet unknown. To address this, the gene expression profile of S. pyogenes within human macrophages was determined and compared to that of extracellular bacteria using customized microarrays and real-time qRT-PCR. In order to model the early phase of infection involving adaptation to the intracellular compartment, samples were collected 2h post-infection. Microarray analysis revealed that the expression of 145 streptococcal genes was significantly altered in the intracellular environment. The majority of differentially regulated genes were associated with metabolic and energy-dependent processes. Key up-regulated genes in early phase intracellular bacteria were ihk and irr, encoding a two-component gene regulatory system (TCS). Comparison of gene expression of selected genes at 2h and 6h post-infection revealed a dramatic shift in response regulators over time with a down-regulation of ihk/irr genes concurring with an up-regulation of the covR/S TCS. In re-infection assays, intracellular bacteria from the 6h time point exhibited significantly greater survival within macrophages than did bacteria collected at the 2h time point. An isogenic S. pyogenes mutant deficient in ihk/irr displayed significantly reduced bacterial counts when compared to wild-type bacteria following infection of macrophages. The findings illustrate how gene expression of S. pyogenes during the intracellular life cycle is fine-tuned by temporal expression of specific two-component systems.
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Affiliation(s)
- Erika Hertzén
- Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Linda Johansson
- Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rita Kansal
- The Cincinnati A Medical Center and the Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Alexander Hecht
- Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Samira Dahesh
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Marton Janos
- Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Malak Kotb
- The Cincinnati A Medical Center and the Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Anna Norrby-Teglund
- Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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