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Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, Da'as MSJ, Abu Kwaik Y. Amoebae as training grounds for microbial pathogens. mBio 2024:e0082724. [PMID: 38975782 DOI: 10.1128/mbio.00827-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.
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Affiliation(s)
- Christopher T D Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Hannah E Hanford
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Tasneem Al-Quadan
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | | | - Cheon J Shin
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Manal S J Da'as
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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2
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Marti H, Suchland RJ, Rockey DD. The Impact of Lateral Gene Transfer in Chlamydia. Front Cell Infect Microbiol 2022; 12:861899. [PMID: 35321311 PMCID: PMC8936141 DOI: 10.3389/fcimb.2022.861899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Lateral gene transfer (LGT) facilitates many processes in bacterial ecology and pathogenesis, especially regarding pathogen evolution and the spread of antibiotic resistance across species. The obligate intracellular chlamydiae, which cause a range of diseases in humans and animals, were historically thought to be highly deficient in this process. However, research over the past few decades has demonstrated that this was not the case. The first reports of homologous recombination in the Chlamydiaceae family were published in the early 1990s. Later, the advent of whole-genome sequencing uncovered clear evidence for LGT in the evolution of the Chlamydiaceae, although the acquisition of tetracycline resistance in Chlamydia (C.) suis is the only recent instance of interphylum LGT. In contrast, genome and in vitro studies have shown that intraspecies DNA exchange occurs frequently and can even cross species barriers between closely related chlamydiae, such as between C. trachomatis, C. muridarum, and C. suis. Additionally, whole-genome analysis led to the identification of various DNA repair and recombination systems in C. trachomatis, but the exact machinery of DNA uptake and homologous recombination in the chlamydiae has yet to be fully elucidated. Here, we reviewed the current state of knowledge concerning LGT in Chlamydia by focusing on the effect of homologous recombination on the chlamydial genome, the recombination machinery, and its potential as a genetic tool for Chlamydia.
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Affiliation(s)
- Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Hanna Marti,
| | - Robert J. Suchland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
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Shala-Lawrence A, Bragagnolo N, Nowroozi-Dayeni R, Kheyson S, Audette GF. The interaction of TraW and TrbC is required to facilitate conjugation in F-like plasmids. Biochem Biophys Res Commun 2018; 503:2386-2392. [PMID: 29966652 DOI: 10.1016/j.bbrc.2018.06.166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/20/2022]
Abstract
Bacterial conjugation, such as that mediated by the E. coli F plasmid, is a main mechanism driving bacterial evolution. Two important proteins required for F-pilus assembly and DNA transfer proficiency are TraW and TrbC. As members of a larger complex, these proteins assemble into a type IV secretion system and are essential components of pore formation and mating pair stabilization between the donor and the recipient cells. In the current report, we demonstrate the physical interaction of TraW and TrbC, show that TraW preferentially interacts with the N-terminal domain of TrbC, and that this interaction is important in restoring conjugation in traW/trbC knockouts.
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Affiliation(s)
- Agnesa Shala-Lawrence
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Nicholas Bragagnolo
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Roksana Nowroozi-Dayeni
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Sasha Kheyson
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Gerald F Audette
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.
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Pillonel T, Bertelli C, Greub G. Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. Front Microbiol 2018. [PMID: 29515524 PMCID: PMC5826181 DOI: 10.3389/fmicb.2018.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Vouga M, Baud D, Greub G. Simkania negevensis, an insight into the biology and clinical importance of a novel member of the Chlamydiales order. Crit Rev Microbiol 2016; 43:62-80. [PMID: 27786615 DOI: 10.3109/1040841x.2016.1165650] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Simkania negevensis is a Chlamydia-related bacterium discovered in 1993 and represents the founding member of the Simkaniaceae family within the Chlamydiales order. As other Chlamydiales, it is an obligate intracellular bacterium characterized by a biphasic developmental cycle. Its similarities with the pathogenic Chlamydia trachomatis and Chlamydia pneumoniae make it an interesting bacterium. So far, little is known about its biology, but S. negevensis harbors various microbiological characteristics of interest, including a strong association of the Simkania-containing vacuole with the ER and the presence of an intron in the 23S rRNA encoding gene. Evidence of human exposition has been reported worldwide. However, there is a lack of robust clinical studies evaluating its implication in human diseases; current data suggest an association with pneumonia and bronchiolitis making S. negevensis a potential emerging pathogen. Owing to its fastidious growth requirements, the clinical relevance of S. negevensis is probably underestimated. In this review, we summarize the current knowledge on S. negevensis and explore future research challenges.
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Affiliation(s)
- Manon Vouga
- a Institute of Microbiology , Center for Research on Intracellular Bacteria, Faculty of Biology and Medicine, University and University Hospital of Lausanne , Lausanne , Switzerland.,b Department "Femme-Mère-Enfant" , Materno-Fetal and Obstetrics Research Unit, University Hospital , Lausanne , Switzerland
| | - David Baud
- a Institute of Microbiology , Center for Research on Intracellular Bacteria, Faculty of Biology and Medicine, University and University Hospital of Lausanne , Lausanne , Switzerland.,b Department "Femme-Mère-Enfant" , Materno-Fetal and Obstetrics Research Unit, University Hospital , Lausanne , Switzerland
| | - Gilbert Greub
- a Institute of Microbiology , Center for Research on Intracellular Bacteria, Faculty of Biology and Medicine, University and University Hospital of Lausanne , Lausanne , Switzerland.,c Infectious Diseases Unit , University hospital , Lausanne , Switzerland
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6
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Bertelli C, Cissé OH, Rusconi B, Kebbi-Beghdadi C, Croxatto A, Goesmann A, Collyn F, Greub G. CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium. Genome Biol Evol 2016; 8:2376-86. [PMID: 27516530 PMCID: PMC5010888 DOI: 10.1093/gbe/evw138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, we describe the presence of a clustered regularly interspaced short palindromic repeats (CRISPR) system, the immune system of bacteria, located on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and associated cas-cse genes of the subtype I-E. A CRISPR locus is also present within Chlamydia sp. Diamant, another Pr. naegleriophila strain, suggesting that the CRISPR system was acquired by a common ancestor of Pr. naegleriophila, after its divergence from Pr. amoebophila. Both nucleotide bias and comparative genomics approaches identified probable horizontal gene acquisitions within two and four genomic islands in Pr. naegleriophila KNic and Diamant genomes, respectively. The plasmid encodes an F-type conjugative system highly similar to 1) that found in the Pam100G genomic island of Pr. amoebophila UWE25 chromosome, as well as on the plasmid of Rubidus massiliensis and 2) to the three genes remaining in the chromosome of Parachlamydia acanthamoebae strains. Therefore, this conjugative system was likely acquired on an ancestral plasmid before the divergence of Parachlamydiaceae Overall, this new complete Pr. naegleriophila genome sequence enables further investigation of the dynamic processes shaping the genomes of the family Parachlamydiaceae and the genus Protochlamydia.
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ousmane H Cissé
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Brigida Rusconi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Antony Croxatto
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Germany
| | - François Collyn
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
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7
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de Brito DM, Maracaja-Coutinho V, de Farias ST, Batista LV, do Rêgo TG. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm. PLoS One 2016; 11:e0146352. [PMID: 26731657 PMCID: PMC4711805 DOI: 10.1371/journal.pone.0146352] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023] Open
Abstract
Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP—Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me.
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Affiliation(s)
- Daniel M. de Brito
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil
- Instituto Vandique, João Pessoa, Brazil
- Beagle Bioinformatics, Santiago, Chile
| | - Savio T. de Farias
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Leonardo V. Batista
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Thaís G. do Rêgo
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
- * E-mail:
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8
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Ball SG, Greub G. Blurred pictures from the crime scene: the growing case for a function of Chlamydiales in plastid endosymbiosis. Microbes Infect 2015; 17:723-6. [DOI: 10.1016/j.micinf.2015.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/12/2022]
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Lamoth F, Pillonel T, Greub G. Waddlia: An emerging pathogen and a model organism to study the biology of chlamydiae. Microbes Infect 2015; 17:732-7. [PMID: 26432516 DOI: 10.1016/j.micinf.2015.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 10/23/2022]
Abstract
Waddlia chondrophila is an emerging pathogen associated with abortion in cattle. In humans, a growing body of evidence supports its pathogenic role in miscarriage and in respiratory tract infection. The human pathogenicity of W. chondrophila is further supported by the presence of several virulence factors including a catalase, a functional T3SS and several adhesins. Despite this medical importance, no commercial tests are available and diagnostic of this strict intracellular bacterium mainly relies on serology, PCR and immunohistochemistry. So far, the epidemiology of W. chondrophila remains largely unexplored and zoonotic, waterborne or interhuman transmission has been considered. Apart from its pathogenic role, chlamydiologists are also interested in W. chondrophila in order to better understand biological mechanisms conserved and shared with Chlamydia spp. Indeed, W. chondrophila proved to be a useful model organism to study the pathobiology of chlamydiae thanks to its rapid replication, its large size allowing precise subcellular protein localization, as well as its growth in Dictyostelium amoebae.
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Affiliation(s)
- Fréderic Lamoth
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland.
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10
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Ruffner B, Péchy-Tarr M, Höfte M, Bloemberg G, Grunder J, Keel C, Maurhofer M. Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus. BMC Genomics 2015; 16:609. [PMID: 26275815 PMCID: PMC4542124 DOI: 10.1186/s12864-015-1763-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/09/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. RESULTS Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. CONCLUSIONS Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.
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Affiliation(s)
- Beat Ruffner
- Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092, Zurich, Switzerland.
| | - Maria Péchy-Tarr
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Crop Protection, Ghent University, Ghent, Belgium.
| | - Guido Bloemberg
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | - Jürg Grunder
- Natural Resources Sciences, University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.
| | - Monika Maurhofer
- Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092, Zurich, Switzerland.
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11
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Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Front Microbiol 2015; 6:101. [PMID: 25745418 PMCID: PMC4333871 DOI: 10.3389/fmicb.2015.00101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/26/2015] [Indexed: 12/25/2022] Open
Abstract
With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | - Sébastien Aeby
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
| | | | - James Clulow
- School of Biology, University of Lausanne Lausanne, Switzerland
| | | | - Samuel Rappo
- School of Biology, University of Lausanne Lausanne, Switzerland
| | | | | | | | - Paola Benaglio
- Department of Medical Genetics, University of Lausanne Lausanne, Switzerland
| | - Laurent Falquet
- Division of Biochemistry, Department of Biology, University of Fribourg Fribourg, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | | | - Walid H Gharib
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany
| | - Keith Harshman
- Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland
| | - Burkhard Linke
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany
| | - Ryo Miyazaki
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | | | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
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12
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Taylor-Brown A, Vaughan L, Greub G, Timms P, Polkinghorne A. Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae. Pathog Dis 2014; 73:1-15. [PMID: 25854000 DOI: 10.1093/femspd/ftu009] [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] [Accepted: 10/29/2014] [Indexed: 11/13/2022] Open
Abstract
Chlamydiae are obligate intracellular bacteria that share a unique but remarkably conserved biphasic developmental cycle that relies on a eukaryotic host cell for survival. Although the phylum was originally thought to only contain one family, the Chlamydiaceae, a total of nine families are now recognized. These so-called Chlamydia-like organisms (CLOs) are also referred to as 'environmental chlamydiae', as many were initially isolated from environmental sources. However, these organisms are also emerging pathogens, as many, such as Parachlamydia sp., Simkania sp. and Waddlia sp., have been associated with human disease, and others, such as Piscichlamydia sp. and Parilichlamydia sp., have been documented in association with diseases in animals. Their strict intracellular nature and the requirement for cell culture have been a confounding factor in characterizing the biology and pathogenicity of CLOs. Nevertheless, the genomes of seven CLO species have now been sequenced, providing new information on their potential ability to adapt to a wide range of hosts. As new isolation and diagnostic methods advance, we are able to further explore the richness of this phylum with further research likely to help define the true pathogenic potential of the CLOs while also providing insight into the origins of the 'traditional' chlamydiae.
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Affiliation(s)
- Alyce Taylor-Brown
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
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Kebbi-Beghdadi C, Greub G. Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:309-24. [PMID: 24992529 DOI: 10.1111/1758-2229.12155] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/14/2014] [Accepted: 02/16/2014] [Indexed: 05/23/2023]
Abstract
Free-living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba-resisting microorganisms (ARMs), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as Legionella and Mycobacteria, and also several newly discovered Chlamydia-related bacteria, such as Parachlamydia acanthamoebae, Estrella lausannensis, Simkania negevensis or Waddlia chondrophila whose pathogenic role towards human or animal is strongly suspected. Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other ARMs and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast-growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that ARMs are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the Chlamydiales order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell-culture-based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.
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Affiliation(s)
- Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
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Bellanger X, Payot S, Leblond-Bourget N, Guédon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 2014; 38:720-60. [DOI: 10.1111/1574-6976.12058] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022] Open
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15
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Ishida K, Sekizuka T, Hayashida K, Matsuo J, Takeuchi F, Kuroda M, Nakamura S, Yamazaki T, Yoshida M, Takahashi K, Nagai H, Sugimoto C, Yamaguchi H. Amoebal endosymbiont Neochlamydia genome sequence illuminates the bacterial role in the defense of the host amoebae against Legionella pneumophila. PLoS One 2014; 9:e95166. [PMID: 24747986 PMCID: PMC3991601 DOI: 10.1371/journal.pone.0095166] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 03/24/2014] [Indexed: 11/19/2022] Open
Abstract
Previous work has shown that the obligate intracellular amoebal endosymbiont Neochlamydia S13, an environmental chlamydia strain, has an amoebal infection rate of 100%, but does not cause amoebal lysis and lacks transferability to other host amoebae. The underlying mechanism for these observations remains unknown. In this study, we found that the host amoeba could completely evade Legionella infection. The draft genome sequence of Neochlamydia S13 revealed several defects in essential metabolic pathways, as well as unique molecules with leucine-rich repeats (LRRs) and ankyrin domains, responsible for protein-protein interaction. Neochlamydia S13 lacked an intact tricarboxylic acid cycle and had an incomplete respiratory chain. ADP/ATP translocases, ATP-binding cassette transporters, and secretion systems (types II and III) were well conserved, but no type IV secretion system was found. The number of outer membrane proteins (OmcB, PomS, 76-kDa protein, and OmpW) was limited. Interestingly, genes predicting unique proteins with LRRs (30 genes) or ankyrin domains (one gene) were identified. Furthermore, 33 transposases were found, possibly explaining the drastic genome modification. Taken together, the genomic features of Neochlamydia S13 explain the intimate interaction with the host amoeba to compensate for bacterial metabolic defects, and illuminate the role of the endosymbiont in the defense of the host amoebae against Legionella infection.
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Affiliation(s)
- Kasumi Ishida
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Fumihiko Takeuchi
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomohiro Yamazaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mitsutaka Yoshida
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Takahashi
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hiroki Nagai
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Chihiro Sugimoto
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
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Zhang R, Zhang CT. A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics 2014; 15:78-94. [PMID: 24822026 PMCID: PMC4009844 DOI: 10.2174/1389202915999140328162433] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022] Open
Abstract
In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.
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Affiliation(s)
- Ren Zhang
- Center for Molecular Medicine and Genetics, Wayne State University Medical School, Detroit, MI 48201, USA
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, China
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Subtil A, Collingro A, Horn M. Tracing the primordial Chlamydiae: extinct parasites of plants? TRENDS IN PLANT SCIENCE 2014; 19:36-43. [PMID: 24210739 DOI: 10.1016/j.tplants.2013.10.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/09/2013] [Accepted: 10/15/2013] [Indexed: 06/02/2023]
Abstract
Chlamydiae are obligate intracellular bacteria found as symbionts and pathogens in a wide range of eukaryotes, including protists, invertebrates, and vertebrates. It was recently proposed that an ancient chlamydial symbiont facilitated the establishment of primary plastids in a tripartite symbiosis with cyanobacteria and early eukaryotes. In this review, we summarize recent advances in understanding of the lifestyle and the evolutionary history of extant Chlamydiae. We reconstruct and describe key features of the ancient chlamydial symbiont. We propose that it was already adapted to an intracellular lifestyle before the emergence of Archaeplastida, and that several observations are compatible with an essential contribution of Chlamydiae to the evolution of algae and plants.
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Affiliation(s)
- Agathe Subtil
- Institut Pasteur, Unité de Biologie des Interactions Cellulaires, Paris, France; CNRS URA2582, Paris, France.
| | - Astrid Collingro
- University of Vienna, Division of Microbial Ecology, Vienna, Austria
| | - Matthias Horn
- University of Vienna, Division of Microbial Ecology, Vienna, Austria
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18
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Matsuo J, Nakamura S, Ito A, Yamazaki T, Ishida K, Hayashi Y, Yoshida M, Takahashi K, Sekizuka T, Takeuchi F, Kuroda M, Nagai H, Hayashida K, Sugimoto C, Yamaguchi H. Protochlamydia induces apoptosis of human HEp-2 cells through mitochondrial dysfunction mediated by chlamydial protease-like activity factor. PLoS One 2013; 8:e56005. [PMID: 23409113 PMCID: PMC3569409 DOI: 10.1371/journal.pone.0056005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/04/2013] [Indexed: 11/22/2022] Open
Abstract
Obligate amoebal endosymbiotic bacterium Protochlamydia with ancestral pathogenic chlamydial features evolved to survive within protist hosts, such as Acanthamoba, 0.7–1.4 billion years ago, but not within vertebrates including humans. This observation raises the possibility that interactions between Protochlamydia and human cells may result in a novel cytopathic effect, leading to new insights into host-parasite relationships. Previously, we reported that Protochlamydia induces apoptosis of the immortalized human cell line, HEp-2. In this study, we attempted to elucidate the molecular mechanism underlying this apoptosis. We first confirmed that, upon stimulation with the bacteria, poly (ADP-ribose) polymerase (PARP) was cleaved at an early stage in HEp-2 cells, which was dependent on the amount of bacteria. A pan-caspase inhibitor and both caspase-3 and -9 inhibitors similarly inhibited the apoptosis of HEp-2 cells. A decrease of the mitochondrial membrane potential was also confirmed. Furthermore, lactacystin, an inhibitor of chlamydial protease-like activity factor (CPAF), blocked the apoptosis. Cytochalasin D also inhibited the apoptosis, which was dependent on the drug concentration, indicating that bacterial entry into cells was required to induce apoptosis. Interestingly, Yersinia type III inhibitors (ME0052, ME0053, and ME0054) did not have any effect on the apoptosis. We also confirmed that the Protochlamydia used in this study possessed a homologue of the cpaf gene and that two critical residues, histidine-101 and serine-499 of C. trachomatis CPAF in the active center, were conserved. Thus, our results indicate that after entry, Protochlamydia-secreted CPAF induces mitochondrial dysfunction with a decrease of the membrane potential, followed by caspase-9, caspase-3 and PARP cleavages for apoptosis. More interestingly, because C. trachomatis infection can block the apoptosis, our finding implies unique features of CPAF between pathogenic and primitive chlamydiae.
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Affiliation(s)
- Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Ito
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Tomohiro Yamazaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kasumi Ishida
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yasuhiro Hayashi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mitsutaka Yoshida
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Takahashi
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Fumihiko Takeuchi
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hiroki Nagai
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Chihiro Sugimoto
- Research Center for Zoonosis Control, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
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Bertelli C, Greub G. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms. Front Cell Infect Microbiol 2012; 2:110. [PMID: 22919697 PMCID: PMC3423634 DOI: 10.3389/fcimb.2012.00110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 08/01/2012] [Indexed: 12/05/2022] Open
Abstract
Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
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20
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Prediction of genomic islands in three bacterial pathogens of pneumonia. Int J Mol Sci 2012; 13:3134-3144. [PMID: 22489145 PMCID: PMC3317706 DOI: 10.3390/ijms13033134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 02/20/2012] [Accepted: 03/01/2012] [Indexed: 11/23/2022] Open
Abstract
Pneumonia is one kind of common infectious disease, which is usually caused by bacteria, viruses, or fungi. In this paper, we predicted genomic islands in three bacterial pathogens of pneumonia. They are Chlamydophila pneumoniae, Mycoplasma pneumoniae and Streptococcus pneumoniae, respectively. For each pathogen, one clinical strain is involved. After implementing the cumulative GC profile combined with h and BCN index, eight genomic islands are found in three pathogens. Among them, six genomic islands are found to have mobility elements, which constitute a kind of conserved character of genomic islands, and this introduces the possibility that they are genuine genomic islands. The present results show that the cumulative GC profile when combined with h and BCN indexes is a good method for predicting genomic islands in bacteria and it has lower false positive rate than the SIGI method. Specially, three genomic islands are found to contain clusters of genes coding for production of virulence factors and this is useful for research into the pathogenicity of these pathogens and helpful for the treatment of diseases caused by them.
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Taylor M, Mediannikov O, Raoult D, Greub G. Endosymbiotic bacteria associated with nematodes, ticks and amoebae. ACTA ACUST UNITED AC 2011; 64:21-31. [PMID: 22126456 DOI: 10.1111/j.1574-695x.2011.00916.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 01/20/2023]
Abstract
Endosymbiosis is a mutualistic, parasitic or commensal symbiosis in which one symbiont is living within the body of another organism. Such symbiotic relationship with free-living amoebae and arthropods has been reported with a large biodiversity of microorganisms, encompassing various bacterial clades and to a lesser extent some fungi and viruses. By contrast, current knowledge on symbionts of nematodes is still mainly restricted to Wolbachia and its interaction with filarial worms that lead to increased pathogenicity of the infected nematode. In this review article, we aim to highlight the main characteristics of symbionts in term of their ecology, host cell interactions, parasitism and co-evolution, in order to stimulate future research in a field that remains largely unexplored despite the availability of modern tools.
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Affiliation(s)
- Mark Taylor
- Molecular and Biochemical Parasitology Group, Liverpool School of Tropical Medicine, Liverpool, UK
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Gimenez G, Bertelli C, Moliner C, Robert C, Raoult D, Fournier PE, Greub G. Insight into cross-talk between intra-amoebal pathogens. BMC Genomics 2011; 12:542. [PMID: 22047552 PMCID: PMC3220658 DOI: 10.1186/1471-2164-12-542] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 11/02/2011] [Indexed: 11/17/2022] Open
Abstract
Background Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to different bacterial phyla and often show a larger genome size than human-infecting pathogens. This characteristic is proposed to be the result of frequent gene exchanges with other bacteria that share a sympatric lifestyle and contrasts with the genome reduction observed among strict human pathogens. Results We sequenced the genome of a new amoebal pathogen, Legionella drancourtii, and compared its gene content to that of a Chlamydia-related bacterium, Parachlamydia acanthamoebae. Phylogenetic reconstructions identified seven potential horizontal gene transfers (HGTs) between the two amoeba-resistant bacteria, including a complete operon of four genes that encodes an ABC-type transporter. These comparisons pinpointed potential cases of gene exchange between P. acanthamoebae and Legionella pneumophila, as well as gene exchanges between other members of the Legionellales and Chlamydiales orders. Moreover, nine cases represent possible HGTs between representatives from the Legionellales or Chlamydiales and members of the Rickettsiales order. Conclusions This study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle.
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Affiliation(s)
- Gregory Gimenez
- Unité des rickettsies, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Wei W, Guo FB. Prediction of genomic islands in seven human pathogens using the Z-Island method. GENETICS AND MOLECULAR RESEARCH 2011; 10:2307-15. [PMID: 22002124 DOI: 10.4238/2011.october.5.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We adopted the method of Zhang and Zhang (the Z-Island method) to identify genomic islands in seven human pathogens, analyzing their chromosomal DNA sequences. The Z-Island method is a theoretical method for predicting genomic islands in bacterial genomes; it consists of determination of the cumulative GC profile and computation of codon usage bias. Thirty-one genomic islands were found in seven pathogens using this method. Further analysis demonstrated that most have the known conserved features; this increases the probability that they are real genomic islands. Eleven genomic islands were found to code for products involved in causing disease (virulence factors) or in resistance to antibiotics (resistance factors). This finding could be useful for research on the pathogenicity of these bacteria and helpful in the treatment of the diseases that they cause. In a comparison of the distribution of mobility elements in genomic islands predicted by different methods, the Z-Island method gave lower false-positive rates. The Z-Island method was found to detect more known genomic islands than the two methods that we compared it with, SIGI-HMM and IslandPick. Furthermore, it maintained a better balance between specificity and sensitivity. The only inconvenience is that the steps for finding genomic islands by the Z-Island method are semi-automatic.
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Affiliation(s)
- W Wei
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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Bellanger X, Morel C, Gonot F, Puymege A, Decaris B, Guédon G. Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture. Mol Microbiol 2011; 81:912-25. [PMID: 21722203 DOI: 10.1111/j.1365-2958.2011.07737.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Genomic islands, flanked by attachment sites, devoid of conjugation and recombination modules and related to the integrative and conjugative element (ICE) ICESt3, were previously found in Streptococcus thermophilus. Here, we show that ICESt3 transfers to a recipient harbouring a similar engineered genomic island, CIMEL₃catR₃, and integrates by site-specific recombination into its attachment sites, leading to their accretion. The resulting composite island can excise, showing that ICESt3 mobilizes CIMEL₃catR₃, in cis. ICESt3, CIMEL₃catR₃, and the whole composite element can transfer from the strain harbouring the composite structure. The ICESt3 transfer to a recipient bearing CIMEL₃catR₃, can also lead to retromobilization, i.e. its capture by the donor. This is the first demonstration of specific conjugative mobilization of a genomic island in cis and the first report of ICE-mediated retromobilization. CIMEL₃catR₃, would be the prototype of a novel class of non-autonomous mobile elements (CIMEs: CIs mobilizable elements), which hijack the recombination and conjugation machinery of related ICEs to excise, transfer and integrate. Few genome analyses have shown that CIMEs could be widespread and have revealed internal repeats that could result from accretions in numerous genomic islands, suggesting that accretion and cis mobilization have a key role in evolution of genomic islands.
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Affiliation(s)
- Xavier Bellanger
- Nancy-Université, UMR1128 Génétique et Microbiologie, F-54506 Vandœuvre-lès-Nancy, France
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Collingro A, Tischler P, Weinmaier T, Penz T, Heinz E, Brunham RC, Read TD, Bavoil PM, Sachse K, Kahane S, Friedman MG, Rattei T, Myers GSA, Horn M. Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol 2011; 28:3253-70. [PMID: 21690563 DOI: 10.1093/molbev/msr161] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
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Marsh J, Kollipara A, Timms P, Polkinghorne A. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus). BMC Microbiol 2011; 11:77. [PMID: 21496349 PMCID: PMC3101125 DOI: 10.1186/1471-2180-11-77] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 04/18/2011] [Indexed: 01/16/2023] Open
Abstract
Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.
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Affiliation(s)
- James Marsh
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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Bertelli C, Collyn F, Croxatto A, Rückert C, Polkinghorne A, Kebbi-Beghdadi C, Goesmann A, Vaughan L, Greub G. The Waddlia genome: a window into chlamydial biology. PLoS One 2010; 5:e10890. [PMID: 20531937 PMCID: PMC2878342 DOI: 10.1371/journal.pone.0010890] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 05/05/2010] [Indexed: 01/11/2023] Open
Abstract
Growing evidence suggests that a novel member of the Chlamydiales order, Waddlia chondrophila, is a potential agent of miscarriage in humans and abortion in ruminants. Due to the lack of genetic tools to manipulate chlamydia, genomic analysis is proving to be the most incisive tool in stimulating investigations into the biology of these obligate intracellular bacteria. 454/Roche and Solexa/Illumina technologies were thus used to sequence and assemble de novo the full genome of the first representative of the Waddliaceae family, W. chondrophila. The bacteria possesses a 2′116′312bp chromosome and a 15′593 bp low-copy number plasmid that might integrate into the bacterial chromosome. The Waddlia genome displays numerous repeated sequences indicating different genome dynamics from classical chlamydia which almost completely lack repetitive elements. Moreover, W. chondrophila exhibits many virulence factors also present in classical chlamydia, including a functional type III secretion system, but also a large complement of specific factors for resistance to host or environmental stresses. Large families of outer membrane proteins were identified indicating that these highly immunogenic proteins are not Chlamydiaceae specific and might have been present in their last common ancestor. Enhanced metabolic capability for the synthesis of nucleotides, amino acids, lipids and other co-factors suggests that the common ancestor of the modern Chlamydiales may have been less dependent on their eukaryotic host. The fine-detailed analysis of biosynthetic pathways brings us closer to possibly developing a synthetic medium to grow W. chondrophila, a critical step in the development of genetic tools. As a whole, the availability of the W. chondrophila genome opens new possibilities in Chlamydiales research, providing new insights into the evolution of members of the order Chlamydiales and the biology of the Waddliaceae.
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - François Collyn
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Antony Croxatto
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | | | - Adam Polkinghorne
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | | | - Lloyd Vaughan
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Moliner C, Fournier PE, Raoult D. Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 2010. [DOI: 10.1111/j.1574-6976.2009.00209.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Mann S, Chen YPP. Bacterial genomic G+C composition-eliciting environmental adaptation. Genomics 2010; 95:7-15. [DOI: 10.1016/j.ygeno.2009.09.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 08/18/2009] [Accepted: 09/01/2009] [Indexed: 01/12/2023]
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Greub G, Kebbi-Beghdadi C, Bertelli C, Collyn F, Riederer BM, Yersin C, Croxatto A, Raoult D. High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach. PLoS One 2009; 4:e8423. [PMID: 20037647 PMCID: PMC2793016 DOI: 10.1371/journal.pone.0008423] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 11/25/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. METHODS/PRINCIPAL FINDINGS We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. CONCLUSIONS/SIGNIFICANCE This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.
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Affiliation(s)
- Gilbert Greub
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.
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Abstract
Despite using modern microbiological diagnostic approaches, the aetiological agents of pneumonia remain unidentified in about 50% of cases. Some bacteria that grow poorly or not at all in axenic media used in routine clinical bacteriology laboratory but which can develop inside amoebae may be the agents of these lower respiratory tract infections (RTIs) of unexplained aetiology. Such amoebae-resisting bacteria, which coevolved with amoebae to resist their microbicidal machinery, may have developed virulence traits that help them survive within human macrophages, i.e. the first line of innate immune defence in the lung. We review here the current evidence for the emerging pathogenic role of various amoebae-resisting microorganisms as agents of RTIs in humans. Specifically, we discuss the emerging pathogenic roles of Legionella-like amoebal pathogens, novel Chlamydiae (Parachlamydia acanthamoebae, Simkania negevensis), waterborne mycobacteria and Bradyrhizobiaceae (Bosea and Afipia spp.).
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Affiliation(s)
- Frédéric Lamoth
- Infectious Diseases Service, University of Lausanne, Lausanne, Switzerland
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Abstract
Parachlamydia acanthamoebae is a Chlamydia-like organism that easily grows within Acanthamoeba spp. Thus, it probably uses these widespread free-living amoebae as a replicative niche, a cosmopolite aquatic reservoir and a vector. A potential role of P. acanthamoebae as an agent of lower respiratory tract infection was initially suggested by its isolation within an Acanthamoeba sp. recovered from the water of a humidifier during the investigation of an outbreak of fever. Additional serological and molecular-based investigations further supported its pathogenic role, mainly in bronchiolitis, bronchitis, aspiration pneumonia and community-acquired pneumonia. P. acanthamoebae was shown to survive and replicate within human macrophages, lung fibroblasts and pneumocytes. Moreover, this strict intracellular bacterium also causes severe pneumonia in experimentally infected mice, thus fulfilling the third and fourth Koch criteria for a pathogenic role. Consequently, new tools have been developed for the diagnosis of parachlamydial infections. It will be important to routinely search for this emerging agent of pneumonia, as P. acanthamoebae is apparently resistant to quinolones, which are antibiotics often used for the empirical treatment of atypical pneumonia. Other Chlamydia-related bacteria, including Protochlamydia naegleriophila, Simkania negevensis and Waddlia chondrophila, might also cause lung infections. Moreover, several additional novel chlamydiae, e.g. Criblamydia sequanensis and Rhabdochlamydia crassificans, have been discovered and are now being investigated for their human pathogenicity.
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Affiliation(s)
- G Greub
- Centre for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Centre and University of Lausanne, Lausanne, Switzerland.
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Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1. Appl Environ Microbiol 2009; 75:4835-52. [PMID: 19465526 DOI: 10.1128/aem.02874-08] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine bacterium strain MC-1 is a member of the alpha subgroup of the proteobacteria that contains the magnetotactic cocci and was the first member of this group to be cultured axenically. The magnetotactic cocci are not closely related to any other known alphaproteobacteria and are only distantly related to other magnetotactic bacteria. The genome of MC-1 contains an extensive (102 kb) magnetosome island that includes numerous genes that are conserved among all known magnetotactic bacteria, as well as some genes that are unique. Interestingly, certain genes that encode proteins considered to be important in magnetosome assembly (mamJ and mamW) are absent from the genome of MC-1. Magnetotactic cocci exhibit polar magneto-aerotaxis, and the MC-1 genome contains a relatively large number of identified chemotaxis genes. Although MC-1 is capable of both autotrophic and heterotrophic growth, it does not appear to be metabolically versatile, with heterotrophic growth confined to the utilization of acetate. Central carbon metabolism is encoded by genes for the citric acid cycle (oxidative and reductive), glycolysis, and gluconeogenesis. The genome also reveals the presence or absence of specific genes involved in the nitrogen, sulfur, iron, and phosphate metabolism of MC-1, allowing us to infer the presence or absence of specific biochemical pathways in strain MC-1. The pathways inferred from the MC-1 genome provide important information regarding central metabolism in this strain that could provide insights useful for the isolation and cultivation of new magnetotactic bacterial strains, in particular strains of other magnetotactic cocci.
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Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas. Proc Natl Acad Sci U S A 2008; 105:20792-7. [PMID: 19098098 DOI: 10.1073/pnas.0806164106] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genomic islands (GEI) comprise a recently recognized large family of potentially mobile DNA elements and play an important role in the rapid differentiation and adaptation of bacteria. Most importantly, GEIs have been implicated in the acquisition of virulence factors, antibiotic resistances or toxic compound metabolism. Despite detailed information on coding capacities of GEIs, little is known about the regulatory decisions in individual cells controlling GEI transfer. Here, we show how self-transfer of ICEclc, a GEI in Pseudomonas knackmussii B13 is controlled by a series of stochastic processes, the result of which is that only a few percent of cells in a population will excise ICEclc and launch transfer. Stochastic processes have been implicated before in producing bistable phenotypic transitions, such as sporulation and competence development, but never before in horizontal gene transfer (HGT). Bistability is instigated during stationary phase at the level of expression of an activator protein InrR that lays encoded on ICEclc, and then faithfully propagated to a bistable expression of the IntB13 integrase, the enzyme responsible for excision and integration of the ICEclc. Our results demonstrate how GEI of a very widespread family are likely to control their transfer rates. Furthermore, they help to explain why HGT is typically confined to few members within a population of cells. The finding that, despite apparent stochasticity, HGT rates can be modulated by external environmental conditions provides an explanation as to why selective conditions can promote DNA exchange.
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Abstract
Members of the phylum Chlamydiae are obligate intracellular bacteria that were discovered about a century ago. Although Chlamydiae are major pathogens of humans and animals, they were long recognized only as a phylogenetically well-separated, small group of closely related microorganisms. The diversity of chlamydiae, their host range, and their occurrence in the environment had been largely underestimated. Today, several chlamydia-like bacteria have been described as symbionts of free-living amoebae and other eukaryotic hosts. Some of these environmental chlamydiae might also be of medical relevance for humans. Their analysis has contributed to a broader understanding of chlamydial biology and to novel insights into the evolution of these unique microorganisms.
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Affiliation(s)
- Matthias Horn
- Department of Microbial Ecology, University of Vienna, A-1090 Vienna, Austria.
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Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella. Infect Immun 2008; 77:642-56. [PMID: 19047403 DOI: 10.1128/iai.01141-08] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetically distinct isolates of Coxiella burnetii, the cause of human Q fever, display different phenotypes with respect to in vitro infectivity/cytopathology and pathogenicity for laboratory animals. Moreover, correlations between C. burnetii genomic groups and human disease presentation (acute versus chronic) have been described, suggesting that isolates have distinct virulence characteristics. To provide a more-complete understanding of C. burnetii's genetic diversity, evolution, and pathogenic potential, we deciphered the whole-genome sequences of the K (Q154) and G (Q212) human chronic endocarditis isolates and the naturally attenuated Dugway (5J108-111) rodent isolate. Cross-genome comparisons that included the previously sequenced Nine Mile (NM) reference isolate (RSA493) revealed both novel gene content and disparate collections of pseudogenes that may contribute to isolate virulence and other phenotypes. While C. burnetii genomes are highly syntenous, recombination between abundant insertion sequence (IS) elements has resulted in genome plasticity manifested as chromosomal rearrangement of syntenic blocks and DNA insertions/deletions. The numerous IS elements, genomic rearrangements, and pseudogenes of C. burnetii isolates are consistent with genome structures of other bacterial pathogens that have recently emerged from nonpathogens with expanded niches. The observation that the attenuated Dugway isolate has the largest genome with the fewest pseudogenes and IS elements suggests that this isolate's lineage is at an earlier stage of pathoadaptation than the NM, K, and G lineages.
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Abstract
Chlamydiae are obligate intracellular bacteria, parasites of a variety of eukaryotes ranging from amoebae to humans. Among them, the family Parachlamydiaceae comprises endosymbionts of amoebae, mainly Acanthamoeba, currently investigated as emerging pathogens of humans and other vertebrates. 16S rDNA-based PCR culture-independent studies in environmental samples have demonstrated the presence of Chlamydiales in various types of nonmedical habitats. Here we reviewed the biology of the Parachlamydiaceae, and more particularly those studies reporting molecular evidences for their presence in the environment, with a re-analysis of the 16S rDNA phylotypes.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS Chlamydia Research Association, Vandoeuvre-lès-Nancy, France.
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Becker B, Hoef-Emden K, Melkonian M. Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes. BMC Evol Biol 2008; 8:203. [PMID: 18627593 PMCID: PMC2490706 DOI: 10.1186/1471-2148-8-203] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 07/15/2008] [Indexed: 11/10/2022] Open
Abstract
Background Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes). Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further test this hypothesis, an extensive search for proteins of chlamydial origin was performed using several recently sequenced algal genomes and EST databases, and the proteins subjected to phylogenetic analyses. Results A total of 39 proteins of chlamydial origin were retrieved from the photosynthetic eukaryotes analyzed and their identity verified through phylogenetic analyses. The distribution of the chlamydial proteins among four groups of photosynthetic eukaryotes (Viridiplantae, Rhodoplantae, Glaucoplantae, Bacillariophyta) was complex suggesting multiple acquisitions and losses. Evidence is presented that all except one of the chlamydial genes originated from an ancient endosymbiosis of a chlamydial bacterium into the ancestor of the Plantae before their divergence into Viridiplantae, Rhodoplantae and Glaucoplantae, i.e. more than 1.1 BYA. The chlamydial proteins subsequently spread through secondary plastid endosymbioses to other eukaryotes. Of 20 chlamydial proteins recovered from the genomes of two Bacillariophyta, 10 were of rhodoplant, and 10 of viridiplant origin suggesting that they were acquired by two different secondary endosymbioses. Phylogenetic analyses of concatenated sequences demonstrated that the viridiplant secondary endosymbiosis likely occurred before the divergence of Chlorophyta and Streptophyta. Conclusion We identified 39 proteins of chlamydial origin in photosynthetic eukaryotes signaling an ancient invasion of the ancestor of the Plantae by a chlamydial bacterium accompanied by horizontal gene transfer. Subsequently, chlamydial proteins spread through secondary endosymbioses to other eukaryotes. We conclude that intracellular chlamydiae likely persisted throughout the early history of the Plantae donating genes to their hosts that replaced their cyanobacterial/plastid homologs thus shaping early algal/plant evolution before they eventually vanished.
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Affiliation(s)
- Burkhard Becker
- Botanisches Institut, Universität zu Köln, Gyrhofstr. 15, 50931 Köln, Germany.
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Moustafa A, Reyes-Prieto A, Bhattacharya D. Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS One 2008; 3:e2205. [PMID: 18493612 PMCID: PMC2376095 DOI: 10.1371/journal.pone.0002205] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 04/07/2008] [Indexed: 11/19/2022] Open
Abstract
Background The photosynthetic organelle (plastid) originated via primary endosymbiosis in which a phagotrophic protist captured and harnessed a cyanobacterium. The plastid was inherited by the common ancestor of the red, green (including land plants), and glaucophyte algae (together, the Plantae). Despite the critical importance of primary plastid endosymbiosis, its ancient derivation has left behind very few “footprints” of early key events in organelle genesis. Methodology/Principal Findings To gain insights into this process, we conducted an in-depth phylogenomic analysis of genomic data (nuclear proteins) from 17 Plantae species to identify genes of a surprising provenance in these taxa, Chlamydiae bacteria. Previous studies show that Chlamydiae contributed many genes (at least 21 in one study) to Plantae that primarily have plastid functions and were postulated to have played a fundamental role in organelle evolution. Using our comprehensive approach, we identify at least 55 Chlamydiae-derived genes in algae and plants, of which 67% (37/55) are putatively plastid targeted and at least 3 have mitochondrial functions. The remainder of the proteins does not contain a bioinformatically predicted organelle import signal although one has an N-terminal extension in comparison to the Chlamydiae homolog. Our data suggest that environmental Chlamydiae were significant contributors to early Plantae genomes that extend beyond plastid metabolism. The chlamydial gene distribution and protein tree topologies provide evidence for both endosymbiotic gene transfer and a horizontal gene transfer ratchet driven by recurrent endoparasitism as explanations for gene origin. Conclusions/Significance Our findings paint a more complex picture of gene origin than can easily be explained by endosymbiotic gene transfer from an organelle-like point source. These data significantly extend the genomic impact of Chlamydiae on Plantae and show that about one-half (30/55) of the transferred genes are most closely related to sequences emanating from the genome of the only environmental isolate that is currently available. This strain, Candidatus Protochlamydia amoebophila UWE25 is an endosymbiont of Acanthamoeba and likely represents the type of endoparasite that contributed the genes to Plantae.
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Affiliation(s)
- Ahmed Moustafa
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Adrian Reyes-Prieto
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Debashish Bhattacharya
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Guy L. Identification and characterization of pathogenicity and other genomic islands using base composition analyses. Future Microbiol 2007; 1:309-16. [PMID: 17661643 DOI: 10.2217/17460913.1.3.309] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pathogenicity islands (PAIs) are major factors contributing to the pathogenicity of bacteria and to their resistance to antibiotics. In general, genomic islands (GIs), of which PAIs are a subset, increase the fitness of their hosts by providing new functions. With the number of available whole genome sequences growing exponentially, in silico methods have been developed to detect putative PAIs and GIs within them. Compositional methods rely on G+C content differences, codon usage and oligonucleotide biases. Other methods detect the presence of functional elements such as tRNA and mobility genes. Future availability of fast, high-throughput, inexpensive genome sequencing emphasizes the need for user-friendly applications able to detect, characterize and analyze putative GIs and PAIs. It may uncover new aspects of pathogenicity and provide better understanding of the evolution of pathogenic bacteria. These methods will be highly requested when whole genome sequencing technologies will be used by physicians for personal diagnosis.
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Affiliation(s)
- Lionel Guy
- Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, Switzerland.
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Eugster M, Roten CAH, Greub G. Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats. BMC Evol Biol 2007; 7:231. [PMID: 18021397 PMCID: PMC2216083 DOI: 10.1186/1471-2148-7-231] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 11/16/2007] [Indexed: 01/20/2023] Open
Abstract
Background Along the chromosome of the obligate intracellular bacteria Protochlamydia amoebophila UWE25, we recently described a genomic island Pam100G. It contains a tra unit likely involved in conjugative DNA transfer and lgrE, a 5.6-kb gene similar to five others of P. amoebophila: lgrA to lgrD, lgrF. We describe here the structure, regulation and evolution of these proteins termed LGRs since encoded by "Large G+C-Rich" genes. Results No homologs to the whole protein sequence of LGRs were found in other organisms. Phylogenetic analyses suggest that serial duplications producing the six LGRs occurred relatively recently and nucleotide usage analyses show that lgrB, lgrE and lgrF were relocated on the chromosome. The C-terminal part of LGRs is homologous to Leucine-Rich Repeats domains (LRRs). Defined by a cumulative alignment score, the 5 to 18 concatenated octacosapeptidic (28-meric) LRRs of LGRs present all a predicted α-helix conformation. Their closest homologs are the 28-residue RI-like LRRs of mammalian NODs and the 24-meres of some Ralstonia and Legionella proteins. Interestingly, lgrE, which is present on Pam100G like the tra operon, exhibits Pfam domains related to DNA metabolism. Conclusion Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. Our model established on bacterial LRRs can be challenged in eucaryotic proteins carrying less conserved LRRs, such as NOD proteins and Toll-like receptors.
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Affiliation(s)
- Myriam Eugster
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland.
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Heinz E, Kolarov I, Kästner C, Toenshoff ER, Wagner M, Horn M. An Acanthamoeba sp. containing two phylogenetically different bacterial endosymbionts. Environ Microbiol 2007; 9:1604-9. [PMID: 17504498 PMCID: PMC1974821 DOI: 10.1111/j.1462-2920.2007.01268.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acanthamoebae are ubiquitous free-living amoebae and important predators of microbial communities. They frequently contain obligate intracellular bacterial symbionts, which show a worldwide distribution. All Acanthamoeba spp. described so far harboured no or only a single specific endosymbiont phylotype, and in some cases evidence for coevolution between the symbiotic bacteria and the amoeba host has been reported. In this study we have isolated and characterized an Acanthamoeba sp. (strain OEW1) showing a stable symbiotic relationship with two morphologically different endosymbionts. 16S rRNA sequence analysis assigned these symbionts to the candidate genus Procabacter (Betaproteobacteria) and the genus Parachlamydia (Chlamydiae) respectively. Fluorescence in situ hybridization and transmission electron microscopy confirmed the affiliation of the endosymbionts and showed their co-occurrence in the amoeba host cells and their intracellular location within separate compartments enclosed by host-derived membranes. Further analysis of this stable relationship should provide novel insights into the complex interactions of intracellular multiple-partner associations.
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Affiliation(s)
| | | | | | | | | | - Matthias Horn
- For correspondence. E-mail ; Tel. (+43) 1 4277 54393; Fax (+43) 1 4277 54389
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Dugan J, Andersen AA, Rockey DD. Functional characterization of IScs605, an insertion element carried by tetracycline-resistant Chlamydia suis. MICROBIOLOGY-SGM 2007; 153:71-9. [PMID: 17185536 DOI: 10.1099/mic.0.29253-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Stable tetracycline resistance in Chlamydia suis is mediated by a family of genomic islands [the tet(C) islands] that are integrated into the chlamydial chromosome. The tet(C) islands contain several plasmid-specific genes, the tet(C) resistance gene and, in most cases, a novel insertion element (IScs605) encoding two predicted transposases. The hypothesis that IScs605 mediated the integration of the tet(C) resistance islands into the C. suis genome was tested using a plasmid-based transposition system in Escherichia coli. Both high- and medium-copy-number plasmids were used as carriers of IScs605 in these experiments. IScs605 integrated into a target plasmid (pOX38) when delivered by either donor plasmid, and integration of the entire donor plasmid was common. IScs605-mediated integration occurred at many positions within pOX38, with 36 of 38 events adjacent to a 5'-TTCAA-3' sequence. Deletions in each of the candidate transposase genes within IScs605 demonstrated that only one of the two ORFs was necessary for the observed transposition activity and target specificity. Analysis of progeny from the mating assays also indicated that IScs605 can excise following integration into a target DNA, and, in each tested case, the sequence 5'-AATTCAA-3' remained at the site of excision. Collectively, these results are consistent with the nucleotide sequence data collected for the tet(C) islands, and strongly suggest that a transposase within IScs605 is responsible for integration of these genomic islands into the C. suis chromosome.
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Affiliation(s)
- Jae Dugan
- Department of Biomedical Sciences, College of Veterinary Medicine and the Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
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Ogata H, Robert C, Audic S, Robineau S, Blanc G, Fournier PE, Renesto P, Claverie JM, Raoult D. Rickettsia felis, from culture to genome sequencing. Ann N Y Acad Sci 2006; 1063:26-34. [PMID: 16481487 DOI: 10.1196/annals.1355.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rickettsia felis has been recently cultured in XTC2 cells. This allows production of enough bacteria to create a genomic bank and to sequence it. The chromosome of R. felis is longer than that of previously sequenced rickettsiae and it possess 2 plasmids. Microscopically, this bacterium exhibits two forms of pili: one resembles a conjugative pilus and another forms hair-like projections that may play a role in pathogenicity. R. felis also exhibits several copies of ankyrin-repeat genes and tetratricopeptide encoding gene that are specifically linked to pathogenic host-associated bacteria. It also contains toxin-antitoxin system encoding genes that are extremely rare in intracellular bacteria and may be linked to plasmid maintenance.
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Affiliation(s)
- H Ogata
- CNRSIBSM, Information Génomique et Structurale, Marseille, France
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45
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Ogata H, La Scola B, Audic S, Renesto P, Blanc G, Robert C, Fournier PE, Claverie JM, Raoult D. Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet 2006; 2:e76. [PMID: 16703114 PMCID: PMC1458961 DOI: 10.1371/journal.pgen.0020076] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 04/04/2006] [Indexed: 11/18/2022] Open
Abstract
The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several genes usually associated with DNA transfer, suggesting that ancestral rickettsiae might have been endowed with a conjugation apparatus. Here we present the genome sequence of Rickettsia bellii, the earliest diverging species of known rickettsiae. The 1,552,076 base pair-long chromosome does not exhibit the colinearity observed between other rickettsia genomes, and encodes a complete set of putative conjugal DNA transfer genes most similar to homologues found in Protochlamydia amoebophila UWE25, an obligate symbiont of amoebae. The genome exhibits many other genes highly similar to homologues in intracellular bacteria of amoebae. We sought and observed sex pili-like cell surface appendages for R. bellii. We also found that R. bellii very efficiently multiplies in the nucleus of eukaryotic cells and survives in the phagocytic amoeba, Acanthamoeba polyphaga. These results suggest that amoeba-like ancestral protozoa could have served as a genetic "melting pot" where the ancestors of rickettsiae and other bacteria promiscuously exchanged genes, eventually leading to their adaptation to the intracellular lifestyle within eukaryotic cells.
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Affiliation(s)
- Hiroyuki Ogata
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR-2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
- * To whom correspondence should be addressed. E-mail: (HO); (DR)
| | - Bernard La Scola
- Unité des Rickettsies, Centre National de la Recherche Scientifique UMR-6020, IFR-48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Stéphane Audic
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR-2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
| | - Patricia Renesto
- Unité des Rickettsies, Centre National de la Recherche Scientifique UMR-6020, IFR-48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR-2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
| | - Catherine Robert
- Unité des Rickettsies, Centre National de la Recherche Scientifique UMR-6020, IFR-48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Pierre-Edouard Fournier
- Unité des Rickettsies, Centre National de la Recherche Scientifique UMR-6020, IFR-48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR-2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
| | - Didier Raoult
- Unité des Rickettsies, Centre National de la Recherche Scientifique UMR-6020, IFR-48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
- * To whom correspondence should be addressed. E-mail: (HO); (DR)
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Gaillard M, Vallaeys T, Vorhölter FJ, Minoia M, Werlen C, Sentchilo V, Pühler A, van der Meer JR. The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol 2006; 188:1999-2013. [PMID: 16484212 PMCID: PMC1426575 DOI: 10.1128/jb.188.5.1999-2013.2006] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties.
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Affiliation(s)
- Muriel Gaillard
- Department of Fundamental Microbiology, Bātiment Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland
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Collyn F, Guy L, Marceau M, Simonet M, Roten CAH. Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics. Bioinformatics 2005; 22:1072-9. [PMID: 16303795 DOI: 10.1093/bioinformatics/bti793] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics. RESULTS YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.
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Affiliation(s)
- F Collyn
- Inserm E0364--Université de Lille II, Faculté de Médecine Henri Warembourg, Institut Pasteur de Lille 1 rue du Pr Calmette, F-59021 Lille, France
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48
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Wernegreen JJ. For better or worse: genomic consequences of intracellular mutualism and parasitism. Curr Opin Genet Dev 2005; 15:572-83. [PMID: 16230003 DOI: 10.1016/j.gde.2005.09.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 09/30/2005] [Indexed: 10/25/2022]
Abstract
Bacteria that replicate within eukaryotic host cells include a variety of pathogenic and mutualistic species. Early genome data for these intracellular associates suggested they experience continual gene loss, little if any gene acquisition, and minimal recombination in small, isolated populations. This view of reductive evolution is itself evolving as new genome sequences clarify mechanisms and outcomes of diverse intracellular associations. Recently sequenced genomes have confirmed a trajectory of gene loss and exceptional genome stability in long-term, nutritional mutualists and certain pathogens. However, new genome data for the Rickettsiales and Chlamydiales indicate more repeated DNA, a greater abundance of mobile DNA elements, and more labile genome dynamics than previously suspected for ancient intracellular lineages. Surprising discoveries of conjugation machinery in the parasite Rickettsia felis and the amoebae symbiont Parachlamydia sp. suggest that DNA transfer might play key roles in some intracellular taxa.
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Affiliation(s)
- Jennifer J Wernegreen
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
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49
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Guy L, Karamata D, Moreillon P, Roten CAH. Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiol 2005; 5:60. [PMID: 16223444 PMCID: PMC1285363 DOI: 10.1186/1471-2180-5-60] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 10/13/2005] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.
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Affiliation(s)
- Lionel Guy
- Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Karamata
- Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | - Philippe Moreillon
- Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | - Claude-Alain H Roten
- Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, CH-1015 Lausanne, Switzerland
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50
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Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier PE, Parinello H, Claverie JM, Raoult D. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol 2005; 3:e248. [PMID: 15984913 PMCID: PMC1166351 DOI: 10.1371/journal.pbio.0030248] [Citation(s) in RCA: 202] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 05/11/2005] [Indexed: 12/04/2022] Open
Abstract
We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular α-proteobacterium causing spotted fever in humans. Besides a circular chromosome of 1,485,148 bp, R. felis exhibits the first putative conjugative plasmid identified among obligate intracellular bacteria. This plasmid is found in a short (39,263 bp) and a long (62,829 bp) form. R.felis contrasts with previously sequenced Rickettsia in terms of many other features, including a number of transposases, several chromosomal toxin–antitoxin genes, many more spoT genes, and a very large number of ankyrin- and tetratricopeptide-motif-containing genes. Host-invasion-related genes for patatin and RickA were found. Several phenotypes predicted from genome analysis were experimentally tested: conjugative pili and mating were observed, as well as β-lactamase activity, actin-polymerization-driven mobility, and hemolytic properties. Our study demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria. Rickettsia felis is an obligate intracellular bacterium that lives in fleas and causes spotted fever in humans. Its genome sequence provides the first evidence that such bacteria can undergo conjugation.
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Affiliation(s)
- Hiroyuki Ogata
- 1 Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
| | - Patricia Renesto
- 2 Unité des Rickettsies, UMR 6020, IFR 48, CNRS, Faculté de Médecine, Marseille Cedex, France
| | - Stéphane Audic
- 1 Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
| | - Catherine Robert
- 2 Unité des Rickettsies, UMR 6020, IFR 48, CNRS, Faculté de Médecine, Marseille Cedex, France
| | - Guillaume Blanc
- 1 Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
| | - Pierre-Edouard Fournier
- 1 Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
- 2 Unité des Rickettsies, UMR 6020, IFR 48, CNRS, Faculté de Médecine, Marseille Cedex, France
| | - Hugues Parinello
- 2 Unité des Rickettsies, UMR 6020, IFR 48, CNRS, Faculté de Médecine, Marseille Cedex, France
| | - Jean-Michel Claverie
- 1 Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
| | - Didier Raoult
- 2 Unité des Rickettsies, UMR 6020, IFR 48, CNRS, Faculté de Médecine, Marseille Cedex, France
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