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Marshall B, Amritkar K, Wolfe M, Kaçar B, Landick R. Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. Front Microbiol 2023; 14:1286626. [PMID: 38029103 PMCID: PMC10663253 DOI: 10.3389/fmicb.2023.1286626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron-sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron-sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.
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Affiliation(s)
- Bailey Marshall
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Kaustubh Amritkar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael Wolfe
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
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2
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Rasmussen JA, Villumsen KR, Duchêne DA, Puetz LC, Delmont TO, Sveier H, Jørgensen LVG, Præbel K, Martin MD, Bojesen AM, Gilbert MTP, Kristiansen K, Limborg MT. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Commun Biol 2021; 4:579. [PMID: 33990699 PMCID: PMC8121932 DOI: 10.1038/s42003-021-02105-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/14/2021] [Indexed: 11/08/2022] Open
Abstract
Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.
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Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Kasper R Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - David A Duchêne
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara C Puetz
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom O Delmont
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Louise von Gersdorff Jørgensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Copenhagen, Denmark
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anders M Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, BGI-Shenzhen, Shenzhen, China
| | - Morten T Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Luo Y, Li C, Zhou Z, Gong Z, Zhu C, Lei A. Biological functions of IL-17-producing cells in mycoplasma respiratory infection. Immunology 2021; 164:223-230. [PMID: 33930194 DOI: 10.1111/imm.13346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/07/2021] [Accepted: 04/18/2021] [Indexed: 12/17/2022] Open
Abstract
Mycoplasmas are the smallest and simplest bacteria that lack a cell wall but have the capability of self-replication. Among them, Mycoplasma pneumoniae is one of the most common causes of community-acquired pneumonia. The hallmark of mycoplasma respiratory diseases is the persistence of lung inflammation that involves both innate and adaptive immune responses. In recent years, a growing body of evidence demonstrates that IL-17 plays an important role in respiratory mycoplasma infection, and associates with the pathologic outcomes of infection, such as pneumonitis and asthma. Numerous studies have shown that a variety of cells, in particular Th17 cells, in the lung can secrete IL-17 during respiratory mycoplasma infection. In this article, we review the biological functions of distinct IL-17-producing cells in mycoplasma respiratory infection with a focus on the effect of IL-17 on the outcomes of infection.
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Affiliation(s)
- Ying Luo
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation enter for Molecular Target New Drug Study, Hengyang Medical College, Institute of Pathogenic Biology, University of South China, Hengyang, China.,Changsha Central Hospital, University of South China, Changsha, China
| | - Cheng Li
- Changsha Central Hospital, University of South China, Changsha, China
| | - Zhou Zhou
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation enter for Molecular Target New Drug Study, Hengyang Medical College, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Zhande Gong
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation enter for Molecular Target New Drug Study, Hengyang Medical College, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Cuiming Zhu
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation enter for Molecular Target New Drug Study, Hengyang Medical College, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Aihua Lei
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation enter for Molecular Target New Drug Study, Hengyang Medical College, Institute of Pathogenic Biology, University of South China, Hengyang, China
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Gómez Rufo D, García Sánchez E, García Sánchez JE, García Moro M. [Clinical implications of the genus Mycoplasma]. REVISTA ESPANOLA DE QUIMIOTERAPIA 2021; 34:169-184. [PMID: 33735544 PMCID: PMC8179937 DOI: 10.37201/req/014.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Dentro del género Mycoplasma, las especies que tradicionalmente se han relacionado con cuadros infecciosos han sido principalmente M. pneumoniae, M. genitalium, M. hominis o U. urealyticum. Sin embargo, existen otras muchas que están implicadas y, que muchas veces, son desconocidas para los profesionales sanitarios. El objetivo de esta revisión es identificar todas las especies del género Mycoplasma que se han aislado en el hombre y determinar su participación en la patología infecciosa humana.
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Affiliation(s)
| | - E García Sánchez
- Enrique García Sánchez, Departamento de Ciencias Biomédicas. Facultad de Medicina. Universidad de Salamanca. Spain.
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A Metabolic Dependency for Host Isoprenoids in the Obligate Intracellular Pathogen Rickettsia parkeri Underlies a Sensitivity to the Statin Class of Host-Targeted Therapeutics. mSphere 2019; 4:4/6/e00536-19. [PMID: 31722991 PMCID: PMC6854040 DOI: 10.1128/msphere.00536-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Obligate intracellular pathogens, which include viruses as well as certain bacteria and eukaryotes, are a subset of infectious microbes that are metabolically dependent on and unable to grow outside an infected host cell because they have lost or lack essential biosynthetic pathways. In this study, we describe a metabolic dependency of the bacterial pathogen Rickettsia parkeri on host isoprenoid molecules that are used in the biosynthesis of downstream products, including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids, such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent a potential Achilles’ heel and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work supports the potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism. Gram-negative bacteria in the order Rickettsiales have an obligate intracellular growth requirement, and some species cause human diseases such as typhus and spotted fever. The bacteria have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome reduction. However, it remains largely unknown which nutrients they acquire and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. Furthermore, we investigated whether the spotted fever group Rickettsia species Rickettsia parkeri scavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry, we found that infection caused decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that treatment of infected cells with statins, which inhibit host isoprenoid synthesis, prohibited bacterial growth. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting that statins lead to an inhibition of cell wall synthesis. Altogether, our results describe a potential Achilles’ heel of obligate intracellular pathogens that can potentially be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth. IMPORTANCE Obligate intracellular pathogens, which include viruses as well as certain bacteria and eukaryotes, are a subset of infectious microbes that are metabolically dependent on and unable to grow outside an infected host cell because they have lost or lack essential biosynthetic pathways. In this study, we describe a metabolic dependency of the bacterial pathogen Rickettsia parkeri on host isoprenoid molecules that are used in the biosynthesis of downstream products, including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids, such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent a potential Achilles’ heel and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work supports the potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism.
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Kamminga T, Koehorst JJ, Vermeij P, Slagman SJ, Martins Dos Santos VAP, Bijlsma JJE, Schaap PJ. Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life. Front Cell Infect Microbiol 2017; 7:31. [PMID: 28224116 PMCID: PMC5293770 DOI: 10.3389/fcimb.2017.00031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/23/2017] [Indexed: 11/26/2022] Open
Abstract
Mycoplasmas are the smallest self-replicating organisms and obligate parasites of a specific vertebrate host. An in-depth analysis of the functional capabilities of mycoplasma species is fundamental to understand how some of simplest forms of life on Earth succeeded in subverting complex hosts with highly sophisticated immune systems. In this study we present a genome-scale comparison, focused on identification of functional protein domains, of 80 publically available mycoplasma genomes which were consistently re-annotated using a standardized annotation pipeline embedded in a semantic framework to keep track of the data provenance. We examined the pan- and core-domainome and studied predicted functional capability in relation to host specificity and phylogenetic distance. We show that the pan- and core-domainome of mycoplasma species is closed. A comparison with the proteome of the “minimal” synthetic bacterium JCVI-Syn3.0 allowed us to classify domains and proteins essential for minimal life. Many of those essential protein domains, essential Domains of Unknown Function (DUFs) and essential hypothetical proteins are not persistent across mycoplasma genomes suggesting that mycoplasma species support alternative domain configurations that bypass their essentiality. Based on the protein domain composition, we could separate mycoplasma species infecting blood and tissue. For selected genomes of tissue infecting mycoplasmas, we could also predict whether the host is ruminant, pig or human. Functionally closely related mycoplasma species, which have a highly similar protein domain repertoire, but different hosts could not be separated. This study provides a concise overview of the functional capabilities of mycoplasma species, which can be used as a basis to further understand host-pathogen interaction or to design synthetic minimal life.
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Affiliation(s)
- Tjerko Kamminga
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and ResearchWageningen, Netherlands; Bioprocess Technology and Support, MSD Animal HealthBoxmeer, Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research Wageningen, Netherlands
| | - Paul Vermeij
- Discovery and Technology, MSD Animal Health Boxmeer, Netherlands
| | - Simen-Jan Slagman
- Bioprocess Technology and Support, MSD Animal Health Boxmeer, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research Wageningen, Netherlands
| | | | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research Wageningen, Netherlands
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7
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Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. PLoS Comput Biol 2013; 9:e1003208. [PMID: 24039564 PMCID: PMC3764002 DOI: 10.1371/journal.pcbi.1003208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2013] [Indexed: 11/19/2022] Open
Abstract
Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate the methodology, a genome-scale metabolic model for the bacterium Mycoplasma gallisepticum was created. Several reactions not predicted by the genome annotation were postulated and validated via the literature. The model predicted an average growth rate of 0.358±0.12, closely matching the experimentally determined growth rate of M. gallisepticum of 0.244±0.03. This work presents a powerful algorithm for facilitating the identification and curation of previously known and new metabolic pathways, as well as presenting the first genome-scale reconstruction of M. gallisepticum. Flux balance analysis (FBA) is a powerful approach for genome-scale metabolic modeling. It provides metabolic engineers with a tool for manipulating, predicting, and optimizing metabolism for biotechnological and biomedical purposes. However, we posit that it can also be used as tool for fundamental research in understanding and curating metabolic networks. Specifically, by using a genetic algorithm integrated with FBA, we developed a curation approach to identify missing reactions, incomplete reactions, and erroneous reactions. Additionally, it was possible to take advantage of the ensemble information from the genetic algorithm to identify the most critical reactions for curation. We tested our strategy using Mycoplasma gallisepticum as our model organism. Using the genome annotation as the basis, the preliminary genome-scale metabolic model consisted of 446 metabolites involved in 380 reactions. Carrying out our analysis, we found over 80 incorrect reactions and 16 missing reactions. Based upon the guidance of the algorithm, we were able to curate and resolve all discrepancies. The model predicted an average bacterial growth rate of 0.358±0.12 h−1 compared to the experimentally observed 0.244±0.03 h−1. Thus, our approach facilitated the curation of a genome-scale metabolic network and generated a high quality metabolic model.
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Soriano-Sarabia N, Sandvold H, Jomaa H, Kubin T, Bein G, Hackstein H. Primary MHC-class II(+) cells are necessary to promote resting Vδ2 cell expansion in response to (E)-4-hydroxy-3-methyl-but-2-enyl-pyrophosphate and isopentenyl pyrophosphate. THE JOURNAL OF IMMUNOLOGY 2012; 189:5212-22. [PMID: 23105138 DOI: 10.4049/jimmunol.1200093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human Vγ9δ2 (Vδ2) T cells represent a unique effector T cell population in humans and primates detecting nonpeptid phosphoantigens, playing an important role in antimicrobial and antitumor immunity. Currently, it is believed that various leukocyte subsets can promote phosphoantigen-driven Vδ2 cell expansion, but the essential cell type required remains elusive. We have used high purity cell sorting to analyze the cellular requirements for (E)-4-hydroxy-3-methyl-but-2-enyl-pyrophosphate (HMBPP)-driven Vδ2 cell expansion. To our knowledge, we show for the first time that primary human MHC-class II(+) cells are indispensable for HMBPP- and isopentenylpyrophosphate-driven Vδ2 cell expansion. In contrast, MHC-class II(-) cells are unable to promote Vδ2 cell expansion. Moreover, purified primary human TCRαβ(+) T cells, CD4(+), or CD8(+) T cells also failed to promote HMBPP-mediated Vδ2 expansion. Depletion of CD4(+)CD25(+) T cells demonstrated that inability of TCRαβ(+) cells to expand Vδ2 cells was not related to the presence of regulatory T cells. Separation of MHC-class II(+) cells into dendritic cells, monocytes, and B cells revealed that dendritic cells were the most potent Vδ2 expanders. Pulsing experiments demonstrated that HMBPP transforms MHC-class II(+) but not negative cells into Vδ2 expanders. MHC-class II-blocking experiments with mAbs and secondary MHC-class II induction on CD4(+) T cells after CD3/CD28 costimulation indicated that MHC-class II is necessary, but not sufficient to promote Vδ2 expansion. Our results provide novel insight into the primary cell-specific requirements for human Vδ2 expansion.
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Affiliation(s)
- Natalia Soriano-Sarabia
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University Giessen, Member of German Center for Lung Research, D-35390 Giessen, Germany
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Davey MS, Lin CY, Roberts GW, Heuston S, Brown AC, Chess JA, Toleman MA, Gahan CGM, Hill C, Parish T, Williams JD, Davies SJ, Johnson DW, Topley N, Moser B, Eberl M. Human neutrophil clearance of bacterial pathogens triggers anti-microbial γδ T cell responses in early infection. PLoS Pathog 2011; 7:e1002040. [PMID: 21589907 PMCID: PMC3093373 DOI: 10.1371/journal.ppat.1002040] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 03/11/2011] [Indexed: 11/18/2022] Open
Abstract
Human blood Vγ9/Vδ2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vγ9/Vδ2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vγ9/Vδ2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-γ and tumor necrosis factor (TNF)-α. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vγ9/Vδ2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-α dependent proliferation of Vγ9/Vδ2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting γδ T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vγ9/Vδ2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The γδ T cell-driven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of γδ T cells and TNF-α and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive γδ T cells in early infection and suggest novel diagnostic and therapeutic approaches. The immune system of all jawed vertebrates harbors three distinct lymphocyte populations – αβ T cells, γδ T cells and B cells – yet only higher primates including humans possess so-called Vγ9/Vδ2 T cells, an enigmatic γδ T cell subset that uniformly responds to the majority of bacterial pathogens. For reasons that are not understood, this responsiveness is absent in all other animals although they too are constantly exposed to a plethora of potentially harmful micro-organisms. We here investigated how Vγ9/Vδ2 T cells respond to live microbes by mimicking physiological conditions in acute disease. Our experiments demonstrate that Vγ9/Vδ2 T cells recognize a small common molecule released when invading bacteria become ingested and killed by other white blood cells. The stimulation of Vγ9/Vδ2 T cells at the site of infection amplifies the inflammatory response and has important consequences for pathogen clearance and the development of microbe-specific immunity. However, if triggered at the wrong time or the wrong place, this rapid reaction toward bacteria may also lead to inflammation-related damage. These findings improve our insight into the complex cellular interactions in early infection, identify novel biomarkers of diagnostic and predictive value and highlight new avenues for therapeutic intervention.
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Affiliation(s)
- Martin S. Davey
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Chan-Yu Lin
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Gareth W. Roberts
- Institute of Nephrology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sinéad Heuston
- Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland
| | - Amanda C. Brown
- Centre for Immunology and Infectious Disease, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - James A. Chess
- Department of Nephrology, Morriston Hospital, Swansea, United Kingdom
| | - Mark A. Toleman
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Cormac G. M. Gahan
- Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland
| | - Tanya Parish
- Centre for Immunology and Infectious Disease, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - John D. Williams
- Institute of Nephrology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Simon J. Davies
- Department of Nephrology, University Hospital of North Staffordshire, Keele University, Stoke-on-Trent, United Kingdom
| | - David W. Johnson
- Department of Nephrology, Princess Alexandra Hospital, University of Queensland, Brisbane, Australia
- Australia and New Zealand Dialysis Transplant Registry, University of Adelaide, Adelaide, Australia
| | - Nicholas Topley
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Bernhard Moser
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Matthias Eberl
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail:
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Brown AC, Eberl M, Crick DC, Jomaa H, Parish T. The nonmevalonate pathway of isoprenoid biosynthesis in Mycobacterium tuberculosis is essential and transcriptionally regulated by Dxs. J Bacteriol 2010; 192:2424-33. [PMID: 20172995 PMCID: PMC2863480 DOI: 10.1128/jb.01402-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 02/11/2010] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis synthesizes isoprenoids via the nonmevalonate or DOXP pathway. Previous work demonstrated that three enzymes in the pathway (Dxr, IspD, and IspF) are all required for growth in vitro. We demonstrate the essentiality of the key genes dxs1 and gcpE, confirming that the pathway is of central importance and that the second homolog of the synthase (dxs2) cannot compensate for the loss of dxs1. We looked at the effect of overexpression of Dxr, Dxs1, Dxs2, and GcpE on viability and on growth in M. tuberculosis. Overexpression of dxs1 or dxs2 was inhibitory to growth, whereas overexpression of dxr or gcpE was not. Toxicity is likely to be, at least partially, due to depletion of pyruvate from the cells. Overexpression of dxs1 or gcpE resulted in increased flux through the pathway, as measured by accumulation of the metabolite 4-hydroxy-3-methyl-but-2-enyl pyrophosphate. We identified the functional translational start site and promoter region for dxr and demonstrated that it is expressed as part of a polycistronic mRNA with gcpE and two other genes. Increased expression of this operon was seen in cells overexpressing Dxs1, indicating that transcriptional control is effected by the first enzyme of the pathway via an unknown regulator.
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Affiliation(s)
- Amanda C. Brown
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, United Kingdom, Department of Infection, Immunity, and Biochemistry, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg, 35392 Giessen, Germany, Infectious Disease Research Institute, Seattle, Washington 98104
| | - Matthias Eberl
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, United Kingdom, Department of Infection, Immunity, and Biochemistry, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg, 35392 Giessen, Germany, Infectious Disease Research Institute, Seattle, Washington 98104
| | - Dean C. Crick
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, United Kingdom, Department of Infection, Immunity, and Biochemistry, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg, 35392 Giessen, Germany, Infectious Disease Research Institute, Seattle, Washington 98104
| | - Hassan Jomaa
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, United Kingdom, Department of Infection, Immunity, and Biochemistry, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg, 35392 Giessen, Germany, Infectious Disease Research Institute, Seattle, Washington 98104
| | - Tanya Parish
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, United Kingdom, Department of Infection, Immunity, and Biochemistry, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg, 35392 Giessen, Germany, Infectious Disease Research Institute, Seattle, Washington 98104
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11
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Bratlie MS, Johansen J, Drabløs F. Relationship between operon preference and functional properties of persistent genes in bacterial genomes. BMC Genomics 2010; 11:71. [PMID: 20109203 PMCID: PMC2837039 DOI: 10.1186/1471-2164-11-71] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 01/28/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genes in bacteria may be organised into operons, leading to strict co-expression of the genes that participate in the same operon. However, comparisons between different bacterial genomes have shown that much of the operon structure is dynamic on an evolutionary time scale. This indicates that there are opposing effects influencing the tendency for operon formation, and these effects may be reflected in properties like evolutionary rate, complex formation, metabolic pathways and gene fusion. RESULTS We have used multi-species protein-protein comparisons to generate a high-quality set of genes that are persistent in bacterial genomes (i.e. they have close to universal distribution). We have analysed these genes with respect to operon participation and important functional properties, including evolutionary rate and protein-protein interactions. CONCLUSIONS Genes for ribosomal proteins show a very slow rate of evolution. This is consistent with a strong tendency for the genes to participate in operons and for their proteins to be involved in essential and well defined complexes. Persistent genes for non-ribosomal proteins can be separated into two classes according to tendency to participate in operons. Those with a strong tendency for operon participation make proteins with fewer interaction partners that seem to participate in relatively static complexes and possibly linear pathways. Genes with a weak tendency for operon participation tend to produce proteins with more interaction partners, but possibly in more dynamic complexes and convergent pathways. Genes that are not regulated through operons are therefore more evolutionary constrained than the corresponding operon-associated genes and will on average evolve more slowly.
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Affiliation(s)
- Marit S Bratlie
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7006 Trondheim, Norway
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12
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Eberl M, Moser B. Monocytes and gammadelta T cells: close encounters in microbial infection. Trends Immunol 2009; 30:562-8. [PMID: 19853512 DOI: 10.1016/j.it.2009.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Revised: 08/25/2009] [Accepted: 09/01/2009] [Indexed: 11/25/2022]
Abstract
gammadelta T cells comprise an evolutionarily conserved yet poorly understood subset of T cells. Numerous features place these unconventional lymphocytes at the branching point between antigen-presenting cells and natural killer cells of the innate immune system and major-histocompatibility-complex-restricted alphabeta T cells of the adaptive immune system. We propose a role for human Vgamma9/Vdelta2 T cells in the generation of monocyte-derived inflammatory dendritic cells during infection. Our model incorporates the peculiar innate-like specificity of Vgamma9/Vdelta2 T cells for the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), co-recruitment of monocytes and Vgamma9/Vdelta2 T cells to sites of infection, and their crosstalk, with profound consequences for the initiation of antigen-specific alphabeta T-cell responses. Vgamma9/Vdelta2 T cells act thus as a cellular switch between innate and adaptive defence mechanisms.
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Affiliation(s)
- Matthias Eberl
- Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.
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13
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Ali Z, Yan L, Plagman N, Reichenberg A, Hintz M, Jomaa H, Villinger F, Chen ZW. Gammadelta T cell immune manipulation during chronic phase of simian-human immunodeficiency virus infection [corrected] confers immunological benefits. THE JOURNAL OF IMMUNOLOGY 2009; 183:5407-17. [PMID: 19786533 DOI: 10.4049/jimmunol.0901760] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Vgamma2Vdelta2 T cells, a major human gammadelta T cell subset, recognize the phosphoantigen (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) produced by mycobacteria and some opportunistic pathogens, and they contribute to innate/adaptive/homeostatic and anticancer immunity. As initial efforts to explore Vgamma2Vdelta2 T cell-based therapeutics against HIV/AIDS-associated bacterial/protozoal infections and neoplasms, we investigated whether a well-defined HMBPP/IL-2 therapeutic regimen could overcome HIV-mediated immune suppression to massively expand polyfunctional Vgamma2Vdelta2 T cells, and whether such activation/expansion could impact AIDS pathogenesis in simian HIV (SHIV)-infected Chinese rhesus macaques. While HMBPP/IL-2 coadministration during acute or chronic phase of SHIV infection induced massive activation/expansion of Vgamma2Vdelta2 T cells, the consequences of such activation/expansions were different between these two treatment settings. HMBPP/IL-2 cotreatment during acute SHIV infection did not prevent the increases in peak and set-point viral loads or the accelerated disease progression seen with IL-2 treatment alone. In contrast, HMBPP/IL-2 cotreatment during chronic infection did not exacerbate disease, and more importantly it could confer immunological benefits. Surprisingly, although viral antigenic loads were not increased upon HMBPP/IL-2 cotreatment during chronic SHIV infection, HMBPP activation of Vgamma2Vdelta2 T cells boosted HIV Env-specific Ab titers. Such increases in Abs were sustained for >170 days and were immediately preceded by increased production of IFN-gamma, TNF-alpha, IL-4, and IL-10 during peak expansion of Vgamma2Vdelta2 T cells displaying memory phenotypes, as well as the short-term increased effector function of Vgamma2Vdelta2 T cells and CD4(+) and CD8(+) alphabeta T cells producing antimicrobial cytokines. Thus, HMBPP/Vgamma2Vdelta2 T cell-based intervention may potentially be useful for combating neoplasms and HMBPP-producing opportunistic pathogens in chronically HIV-infected individuals.
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Affiliation(s)
- Zahida Ali
- Department of Microbiology and Immunology, Center for Primate Biomedical Research, University of Illinois at Chicago, College of Medicine, Chicago, IL 60612, USA
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14
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Ali Z, Shao L, Halliday L, Reichenberg A, Hintz M, Jomaa H, Chen ZW. Prolonged (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate-driven antimicrobial and cytotoxic responses of pulmonary and systemic Vgamma2Vdelta2 T cells in macaques. THE JOURNAL OF IMMUNOLOGY 2008; 179:8287-96. [PMID: 18056373 DOI: 10.4049/jimmunol.179.12.8287] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although phosphoantigen-specific Vgamma2Vdelta2 T cells appear to play a role in antimicrobial and anticancer immunity, mucosal immune responses and effector functions of these gammadelta T cells during infection or phospholigand treatment remain poorly characterized. In this study, we demonstrate that the microbial phosphoantigen (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) plus IL-2 treatment of macaques induced a prolonged major expansion of circulating Vgamma2Vdelta2 T cells that expressed CD8 and produced cytotoxic perforin during their peak expansion. Interestingly, HMBPP-activated Vgamma2Vdelta2 T cells underwent an extraordinary pulmonary accumulation, which lasted for 3-4 mo, although circulating Vgamma2Vdelta2 T cells had returned to baseline levels weeks prior. The Vgamma2Vdelta2 T cells that accumulated in the lung following HMBPP/IL-2 cotreatment displayed an effector memory phenotype, as follows: CCR5+CCR7-CD45RA-CD27+ and were able to re-recognize phosphoantigen and produce copious amounts of IFN-gamma up to 15 wk after treatment. Furthermore, the capacity of massively expanded Vgamma2Vdelta2 T cells to produce cytokines in vivo coincided with an increase in numbers of CD4+ and CD8+ alphabeta T cells after HMBPP/IL-2 cotreatment as well as substantial perforin expression by CD3+Vgamma2- T cells. Thus, the prolonged HMBPP-driven antimicrobial and cytotoxic responses of pulmonary and systemic Vgamma2Vdelta2 T cells may confer immunotherapeutics against infectious diseases and cancers.
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Affiliation(s)
- Zahida Ali
- Department of Microbiology and Immunology, Center for Primate Biomedical Research, University of Illinois, College of Medicine, Chicago, IL 60612, USA
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15
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Ershov YV. 2-C-methylerythritol phosphate pathway of isoprenoid biosynthesis as a target in identifying new antibiotics, herbicides, and immunomodulators: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807020019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Abstract
In this review, we discuss the potential role of human gammadelta T cells in the control of adaptive immunity. Our latest findings emerged as a consequence of our working hypothesis, which predicts a close relationship between the migration control in leukocytes and their function in immune processes as diverse as hematopoiesis, initiation of adaptive immunity, and immune surveillance in peripheral tissues. Leukocyte migration control is defined by the combination of migration and adhesion receptors on their surface and the tissue distribution of the corresponding ligands. According to our hypothesis, leukocytes featuring migration receptors for homing to lymph nodes (LNs) will also display activities that preferentially take place within LNs. Following this line of thought, by showing LN-homing properties in a subset of human gammadelta T cells, we speculated that gammadelta T cells influence the initiation of T- and B-cell responses. Here, we summarize our recent data, showing that LN-homing gammadelta T cells have potent antigen-presenting cell characteristics. This unexpected finding is discussed with regards to microbial sensing by human gammadelta T cells and a possible role for these cells in anti-microbial immunity.
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Affiliation(s)
- Bernhard Moser
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
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17
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Born WK, Reardon CL, O'Brien RL. The function of gammadelta T cells in innate immunity. Curr Opin Immunol 2005; 18:31-8. [PMID: 16337364 DOI: 10.1016/j.coi.2005.11.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 11/24/2005] [Indexed: 02/06/2023]
Abstract
Many researchers believe that gammadelta T lymphocytes belong somewhere 'in-between' the innate and adaptive immune systems. Recent studies strongly emphasize the innate features and functions of these cells, including the use of germline elements of the T cell receptor for ligand recognition, segregation into functionally specialized cell populations in correlation with T cell receptor variable gene or protein expression, interactions with cells of the innate system at many levels and, the latest addition, the ability to present antigen. Thus, at present, much evidence suggests that gammadelta T cells function in an innate manner, although they are arguably the most complex and advanced cellular representatives of the innate immune system.
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Affiliation(s)
- Willi K Born
- Department of Immunology, at National Jewish Medical and Research Center, 1400 Jackson Street, Denver, CO 80206, USA.
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