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Ardissone S, Greub G. The Chlamydia-related Waddlia chondrophila encodes functional type II toxin-antitoxin systems. Appl Environ Microbiol 2024; 90:e0068123. [PMID: 38214519 PMCID: PMC10880633 DOI: 10.1128/aem.00681-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
Bacterial toxin-antitoxin (TA) systems are widespread in chromosomes and plasmids of free-living microorganisms, but only a few have been identified in obligate intracellular species. We found seven putative type II TA modules in Waddlia chondrophila, a Chlamydia-related species that is able to infect a very broad series of eukaryotic hosts, ranging from protists to mammalian cells. The RNA levels of Waddlia TA systems are significantly upregulated by iron starvation and novobiocin, but they are not affected by antibiotics such as β-lactams and glycopeptides, which suggests different mechanisms underlying stress responses. Five of the identified TA modules, including HigBA1 and MazEF1, encoded on the Waddlia cryptic plasmid, proved to be functional when expressed in a heterologous host. TA systems have been associated with the maintenance of mobile genetic elements, bacterial defense against bacteriophages, and persistence upon exposure to adverse conditions. As their RNA levels are upregulated upon exposure to adverse conditions, Waddlia TA modules may be involved in survival to stress. Moreover, as Waddlia can infect a wide range of hosts including free-living amoebae, TA modules could also represent an innate immunity system to fight against bacteriophages and other microorganisms with which Waddlia has to share its replicative niche.IMPORTANCEThe response to adverse conditions, such as exposure to antibiotics, nutrient starvation and competition with other microorganisms, is essential for the survival of a bacterial population. TA systems are modules composed of two elements, a toxic protein and an antitoxin (protein or RNA) that counteracts the toxin. Although many aspects of TA biological functions still await to be elucidated, TAs have often been implicated in bacterial response to stress, including the response to nutrient starvation, antibiotic treatment and bacteriophage infection. TAs are ubiquitous in free-living bacteria but rare in obligate intracellular species such as chlamydiae. We identified functional TA systems in Waddlia chondrophila, a chlamydial species with a strikingly broad host range compared to other chlamydiae. Our work contributes to understand how obligate intracellular bacteria react to adverse conditions that might arise from competition with other viruses/bacteria for the same replicative niche and would threaten their ability to replicate.
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Affiliation(s)
- Silvia Ardissone
- Institute of Microbiology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
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2
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Rovero A, Kebbi-Beghdadi C, Greub G. Spontaneous Aberrant Bodies Formation in Human Pneumocytes Infected with Estrella lausannensis. Microorganisms 2023; 11:2368. [PMID: 37894026 PMCID: PMC10609161 DOI: 10.3390/microorganisms11102368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Estrella lausannensis, a Chlamydia-related bacterium isolated from a Spanish river, is considered as a possible emerging human pathogen. Indeed, it was recently demonstrated to multiply in human macrophages, resisting oxidative burst and causing a strong cytopathic effect. In addition, a preliminary study highlighted a correlation between antibody response to E. lausannensis and pneumonia in children. To clarify the pathogenic potential of these bacteria, we infected a human pneumocyte cell line with E. lausannensis and assessed its replication and cytopathic effect using quantitative real-time PCR and immunofluorescence, as well as confocal and electron microscopy. Our results demonstrated that E. lausannensis enters and replicates rapidly in human pneumocytes, and that it causes a prompt lysis of the host cells. Furthermore, we reported the spontaneous formation of aberrant bodies, a form associated with persistence in Chlamydiae, suggesting that E. lausannensis infection could cause chronic disorders in humans.
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Affiliation(s)
- Aurelien Rovero
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (A.R.); (C.K.-B.)
| | - Carole Kebbi-Beghdadi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (A.R.); (C.K.-B.)
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (A.R.); (C.K.-B.)
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
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3
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Köstlbacher S, Collingro A, Halter T, Schulz F, Jungbluth SP, Horn M. Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nat Commun 2021; 12:4021. [PMID: 34188040 PMCID: PMC8242063 DOI: 10.1038/s41467-021-24294-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the "Genomes from Earth's Microbiomes" initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.
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Affiliation(s)
- Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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4
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Köstlbacher S, Collingro A, Halter T, Domman D, Horn M. Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria. Curr Biol 2021; 31:346-357.e3. [PMID: 33157023 PMCID: PMC7846284 DOI: 10.1016/j.cub.2020.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022]
Abstract
Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.
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Affiliation(s)
- Stephan Köstlbacher
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria
| | - Astrid Collingro
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria
| | - Tamara Halter
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria
| | - Daryl Domman
- Wellcome Sanger Institute, Parasites and Microbes Programme, Hinxton, Cambridge CB10 1SA, UK; Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria.
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5
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Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG. Marine Sediments Illuminate Chlamydiae Diversity and Evolution. Curr Biol 2020; 30:1032-1048.e7. [PMID: 32142706 DOI: 10.1016/j.cub.2020.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/22/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay 91400, France
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Felix Homa
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Steffen L Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen 5020, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg 1790 AB, the Netherlands
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands.
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6
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Pillonel T, Bertelli C, Aeby S, de Barsy M, Jacquier N, Kebbi-Beghdadi C, Mueller L, Vouga M, Greub G. Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship. Genome Biol Evol 2019; 11:1334-1344. [PMID: 30949677 PMCID: PMC6490308 DOI: 10.1093/gbe/evz072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2019] [Indexed: 12/15/2022] Open
Abstract
The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8,534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of five female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named "Candidatus Rhabdochlamydia helvetica" whereas only few thousand reads mapped to the genome of "Candidatus Midichloria mitochondrii," a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of interphylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales), and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Sébastien Aeby
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Marie de Barsy
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Nicolas Jacquier
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Linda Mueller
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Manon Vouga
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
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7
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Taylor-Brown A, Pillonel T, Greub G, Vaughan L, Nowak B, Polkinghorne A. Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae. Genome Biol Evol 2018; 10:2587-2595. [PMID: 30202970 PMCID: PMC6171736 DOI: 10.1093/gbe/evy195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.
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Affiliation(s)
- Alyce Taylor-Brown
- USC Animal Research Centre, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Switzerland
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Barbara Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, Australia
| | - Adam Polkinghorne
- USC Animal Research Centre, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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8
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Major P, Embley TM, Williams TA. Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes. Genome Biol Evol 2018; 9:480-487. [PMID: 28164241 PMCID: PMC5381601 DOI: 10.1093/gbe/evx015] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 01/24/2023] Open
Abstract
Plasma membrane-located nucleotide transport proteins (NTTs) underpin the lifestyle of important obligate intracellular bacterial and eukaryotic pathogens by importing energy and nucleotides from infected host cells that the pathogens can no longer make for themselves. As such their presence is often seen as a hallmark of an intracellular lifestyle associated with reductive genome evolution and loss of primary biosynthetic pathways. Here, we investigate the phylogenetic distribution of NTT sequences across the domains of cellular life. Our analysis reveals an unexpectedly broad distribution of NTT genes in both host-associated and free-living prokaryotes and eukaryotes. We also identify cases of within-bacteria and bacteria-to-eukaryote horizontal NTT transfer, including into the base of the oomycetes, a major clade of parasitic eukaryotes. In addition to identifying sequences that retain the canonical NTT structure, we detected NTT gene fusions with HEAT-repeat and cyclic nucleotide binding domains in Cyanobacteria, pathogenic Chlamydiae and Oomycetes. Our results suggest that NTTs are versatile functional modules with a much wider distribution and a broader range of potential roles than has previously been appreciated.
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Affiliation(s)
- Peter Major
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Tom A Williams
- School of Earth Sciences, University of Bristol, United Kingdom
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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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10
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Bayramova F, Jacquier N, Greub G. Insight in the biology of Chlamydia-related bacteria. Microbes Infect 2017; 20:432-440. [PMID: 29269129 DOI: 10.1016/j.micinf.2017.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/14/2017] [Accepted: 11/21/2017] [Indexed: 01/21/2023]
Abstract
The Chlamydiales order is composed of obligate intracellular bacteria and includes the Chlamydiaceae family and several family-level lineages called Chlamydia-related bacteria. In this review we will highlight the conserved and distinct biological features between these two groups. We will show how a better characterization of Chlamydia-related bacteria may increase our understanding on the Chlamydiales order evolution, and may help identifying new therapeutic targets to treat chlamydial infections.
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Affiliation(s)
- Firuza Bayramova
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Nicolas Jacquier
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Gilbert Greub
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland.
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11
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Mueller L, Bertelli C, Pillonel T, Salamin N, Greub G. One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions. Genome Biol Evol 2017; 9:1432-1449. [PMID: 28525571 PMCID: PMC5513546 DOI: 10.1093/gbe/evx074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate–protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture.
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Affiliation(s)
- Linda Mueller
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Trestan Pillonel
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland
| | - Nicolas Salamin
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland
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12
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Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M. Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. ISME JOURNAL 2017. [PMID: 28644443 PMCID: PMC5604735 DOI: 10.1038/ismej.2017.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Marc Mussmann
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | | | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias Horn
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
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13
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Cenci U, Bhattacharya D, Weber APM, Colleoni C, Subtil A, Ball SG. Biotic Host-Pathogen Interactions As Major Drivers of Plastid Endosymbiosis. TRENDS IN PLANT SCIENCE 2017; 22:316-328. [PMID: 28089380 DOI: 10.1016/j.tplants.2016.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/21/2016] [Accepted: 12/12/2016] [Indexed: 05/22/2023]
Abstract
The plastid originated 1.5 billion years ago through a primary endosymbiosis involving a heterotrophic eukaryote and an ancient cyanobacterium. Phylogenetic and biochemical evidence suggests that the incipient endosymbiont interacted with an obligate intracellular chlamydial pathogen that housed it in an inclusion. This aspect of the ménage-à-trois hypothesis (MATH) posits that Chlamydiales provided critical novel transporters and enzymes secreted by the pathogens in the host cytosol. This initiated the efflux of photosynthate to both the inclusion lumen and host cytosol. Here we review the experimental evidence supporting the MATH and focus on chlamydial genes that replaced existing cyanobacterial functions. The picture emerging from these studies underlines the importance of chlamydial host-pathogen interactions in the metabolic integration of the primary plastid.
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Affiliation(s)
- Ugo Cenci
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex, France
| | - Debashish Bhattacharya
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany
| | - Christophe Colleoni
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex, France
| | - Agathe Subtil
- Institut Pasteur, Unité de Biologie Cellulaire de l'Infection Microbienne, 25 Rue du Dr Roux, 75015 Paris, France
| | - Steven G Ball
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex, France.
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14
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Taylor-Brown A, Pillonel T, Bridle A, Qi W, Bachmann NL, Miller TL, Greub G, Nowak B, Seth-Smith HMB, Vaughan L, Polkinghorne A. Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria. Environ Microbiol 2017; 19:1899-1913. [PMID: 28205377 DOI: 10.1111/1462-2920.13694] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/12/2022]
Abstract
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridization. Giant grouper (Epinephelus lanceolatus) cultured in the same systems were epitheliocystis free. 16S rRNA gene sequencing revealed a novel member of the Candidatus Parilichlamydiaceae: Ca. Similichlamydia epinephelii. Using metagenomic approaches, we obtained an estimated 68% of the chlamydial genome, revealing that this novel chlamydial pathogen shares a number of key pathogenic hallmarks with the Chlamydiaceae, including an intact Type III Secretion system and several chlamydial virulence factors. This provides additional evidence that these pathogenic mechanisms were acquired early in the evolution of this unique bacterial phylum. The identification and genomic characterization of Ca. S. epinephelii provides new opportunities to study the biology of distantly-related chlamydial pathogens while shining a new light on the evolution of pathogenicity of the Chlamydiaceae.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Andrew Bridle
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia
| | - Weihong Qi
- Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland
| | - Nathan L Bachmann
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Terrence L Miller
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Cairns, Queensland, 4878, Australia
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Barbara Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia
| | - Helena M B Seth-Smith
- Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland.,Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
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15
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Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkova-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR. The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PLoS One 2016; 11:e0165850. [PMID: 27812150 PMCID: PMC5094676 DOI: 10.1371/journal.pone.0165850] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.
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Affiliation(s)
- Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Andrea Komljenovic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Audrey Bourdilloud
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Burkhard Linke
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Keith Harshman
- Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Francisca Segers
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fabien Delapierre
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Damien Fiorucci
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Seppey
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Evgeniya Trofimenco
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Pauline Berra
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Athimed El Taher
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Chloé Loiseau
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Dejan Roggero
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Madeleine Sulfiotti
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angela Etienne
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gustavo Ruiz Buendia
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Loïc Pillard
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angelique Escoriza
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Roxane Moritz
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cedric Schneider
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Esteban Alfonso
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fatma Ben Jeddou
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Oliver Selmoni
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gregory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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16
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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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17
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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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18
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Kebbi-Beghdadi C, Fatton M, Greub G. Permissivity of insect cells to Waddlia chondrophila, Estrella lausannensis and Parachlamydia acanthamoebae. Microbes Infect 2015; 17:749-54. [PMID: 26423021 DOI: 10.1016/j.micinf.2015.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/14/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023]
Abstract
Recent large scale studies questioning the presence of intracellular bacteria of the Chlamydiales order in ticks and fleas revealed that arthropods, similarly to mammals, reptiles, birds or fishes, can be colonized by Chlamydia-related bacteria with a predominant representation of the Rhabdochlamydiaceae and Parachlamydiaceae families. We thus investigated the permissivity of two insect cell lines towards Waddlia chondrophila, Estrella lausannensis and Parachlamydia acanthamoebae, three bacteria representative of three distinct families within the Chlamydiales order, all documented in ticks and/or in other arthropods. We demonstrated that W. chondrophila and E. lausannensis are able to very efficiently multiply in these insect cell lines. E. lausannensis however induced a rapid cytopathic effect, which somehow restricted its replication. P. acanthamoebae was not able to grow in these cell lines even if inclusions containing a few replicating bacteria could occasionally be observed.
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Affiliation(s)
- Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Morgane Fatton
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
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19
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de Barsy M, Bertelli C, Jacquier N, Kebbi-Beghdadi C, Greub G. ESCCAR international congress on Rickettsia and other intracellular bacteria. Microbes Infect 2015; 17:680-8. [PMID: 26297854 DOI: 10.1016/j.micinf.2015.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/08/2015] [Indexed: 11/17/2022]
Abstract
The European Society for the study of Chlamydia, Coxiella, Anaplasma and Rickettsia (ESCCAR) held his triennial international meeting in Lausanne. This meeting gathered 165 scientists from 28 countries and all 5 continents, allowing efficient networking and major scientific exchanges. Topics covered include molecular and cellular microbiology, genomics, as well as epidemiology, veterinary and human medicine. Several breakthroughs have been revealed at the meeting, such as (i) the presence of CRISPR (the "prokaryotic immune system") in chlamydiae, (ii) an Anaplasma effector involved in host chromatin remodelling, (iii) the polarity of the type III secretion system of chlamydiae during the entry process revealed by cryo-electron tomography. Moreover, the ESCCAR meeting was a unique opportunity to be exposed to cutting-edge science and to listen to comprehensive talks on current hot topics.
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Affiliation(s)
- Marie de Barsy
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
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20
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Temple L, Lewis L. Phage on the stage. BACTERIOPHAGE 2015; 5:e1062589. [PMID: 26442195 DOI: 10.1080/21597081.2015.1062589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/05/2015] [Accepted: 06/09/2015] [Indexed: 01/05/2023]
Abstract
The resurgence of interest in bacteriophages for use in combating antibiotic resistant bacteria is coincident with an urgent call for more effective science education practices, including hands-on learning opportunities. To address this issue, a number of solutions have been proposed, including a large educational experiment, begun in 2007 by the Howard Hughes Medical Institute and currently involving over 85 colleges and universities, which has students discovering unique phages, obtaining images, and purifying phage DNA. A subset of these phage genomes is sequenced and analyzed using bioinformatics tools. Papers describing individual phage discoveries and comparative genomic studies are being published regularly. The vast majority of students in the program are in their first year of college, a critical time in capturing their interest and retaining them as science majors. This viral discovery model is being adopted and modified by a wide variety of educational institutions using a number of different bacterial hosts. In the opinion of the authors, this program and others like it represent a model accessible to virtually any undergraduate setting. And because of these programs, bacteriophage enthusiasts (academics, health professionals, biotechnology companies) can look forward to more well prepared students entering their ranks and should anticipate many more potentially useful phages discovered and characterized.
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Affiliation(s)
- Louise Temple
- Department of Integrated Science & Technology; James Madison University ; Harrisonburg, VA USA ; Department of Biological Sciences; University of Mary Washington ; Fredericksburg, VA USA
| | - Lynn Lewis
- Department of Integrated Science & Technology; James Madison University ; Harrisonburg, VA USA ; Department of Biological Sciences; University of Mary Washington ; Fredericksburg, VA USA
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