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Dharamshi JE, Köstlbacher S, Schön ME, Collingro A, Ettema TJG, Horn M. Gene gain facilitated endosymbiotic evolution of Chlamydiae. Nat Microbiol 2023; 8:40-54. [PMID: 36604515 PMCID: PMC9816063 DOI: 10.1038/s41564-022-01284-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Chlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifestyle is still largely unresolved. Here we reconstructed Planctomycetes-Verrucomicrobia-Chlamydiae species relationships and modelled superphylum genome evolution. Gene content reconstruction from 11,996 gene families suggests a motile and facultatively anaerobic last common Chlamydiae ancestor that had already gained characteristic endosymbiont genes. Counter to expectations for genome streamlining in strict endosymbionts, we detected substantial gene gain within Chlamydiae. We found that divergence in energy metabolism and aerobiosis observed in extant lineages emerged later during chlamydial evolution. In particular, metabolic and aerobic genes characteristic of the more metabolically versatile protist-infecting chlamydiae were gained, such as respiratory chain complexes. Our results show that metabolic complexity can increase during endosymbiont evolution, adding an additional perspective for understanding symbiont evolutionary trajectories across the tree of life.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephan Köstlbacher
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Astrid Collingro
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria.
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2
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Gynaecological infections in paediatric and adolescent gynaecology: a review of recommendations. Postepy Dermatol Alergol 2021; 38:734-739. [PMID: 34849117 PMCID: PMC8610037 DOI: 10.5114/ada.2021.110084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 11/17/2022] Open
Abstract
Inflammation within the genital organs in women is an important problem in gynaecology and venereology. Understanding the factors contributing to the inflammatory process and the role of defence mechanisms against their occurrence is important in terms of prevention and treatment. It is especially visible in paediatric gynaecology, where inflammatory diseases of the vulva, dermatoses, injuries and the effects of possible sexual harassment may overlap.
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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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Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont. Proc Natl Acad Sci U S A 2020; 117:21658-21666. [PMID: 32817434 PMCID: PMC7474615 DOI: 10.1073/pnas.2005536117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Symbiotic relationships with microbes are ubiquitous among living beings and can be parasitic, such as in bacterial pathogens, or mutualistic, as in beneficial microbiomes. Among other factors, the outcome of microbe–host relationships is determined by the mode of symbiont transmission from host to host. Here we describe how bacterial symbionts increased in infectivity and virulence toward their amoeba host when transmission to a new host was essential for survival. The enhanced parasitism is a result of genomic changes and a pronounced switch of gene expression altering the symbionts’ mechanisms for host interaction. Our study provides both a molecular explanation as well as a blueprint for how changes in gene expression are sufficient to confer enhanced parasitism in microbes. Symbiosis with microbes is a ubiquitous phenomenon with a massive impact on all living organisms, shaping the world around us today. Theoretical and experimental studies show that vertical transmission of symbionts leads to the evolution of mutualistic traits, whereas horizontal transmission facilitates the emergence of parasitic features. However, these studies focused on phenotypic data, and we know little about underlying molecular changes at the genomic level. Here, we combined an experimental evolution approach with infection assays, genome resequencing, and global gene expression analysis to study the effect of transmission mode on an obligate intracellular bacterial symbiont. We show that a dramatic shift in the frequency of genetic variants, coupled with major changes in gene expression, allow the symbiont to alter its position in the parasitism–mutualism continuum depending on the mode of between-host transmission. We found that increased parasitism in horizontally transmitted chlamydiae residing in amoebae was a result of processes occurring at the infectious stage of the symbiont’s developmental cycle. Specifically, genes involved in energy production required for extracellular survival and the type III secretion system—the symbiont’s primary virulence mechanism—were significantly up-regulated. Our results identify the genomic and transcriptional dynamics sufficient to favor parasitic or mutualistic strategies.
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5
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Chlamydiae in the Environment. Trends Microbiol 2020; 28:877-888. [PMID: 32591108 DOI: 10.1016/j.tim.2020.05.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.
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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: 31] [Impact Index Per Article: 7.8] [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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Abstract
The evolutionary separated Gram-negative Chlamydiales show a biphasic life cycle and replicate exclusively within eukaryotic host cells. Members of the genus Chlamydia are responsible for many acute and chronic diseases in humans, and Chlamydia-related bacteria are emerging pathogens. We revisit past efforts to detect cell wall material in Chlamydia and Chlamydia-related bacteria in the context of recent breakthroughs in elucidating the underlying cellular and molecular mechanisms of the chlamydial cell wall biosynthesis. In this review, we also discuss the role of cell wall biosynthesis in chlamydial FtsZ-independent cell division and immune modulation. In the past, penicillin susceptibility of an invisible wall was referred to as the "chlamydial anomaly." In light of new mechanistic insights, chlamydiae may now emerge as model systems to understand how a minimal and modified cell wall biosynthetic machine supports bacterial cell division and how cell wall-targeting beta-lactam antibiotics can also act bacteriostatically rather than bactericidal. On the heels of these discussions, we also delve into the effects of other cell wall antibiotics in individual chlamydial lineages.
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Abstract
Bacterial pathogens are generally investigated in the context of disease. To prevent outbreaks, it is essential to understand their lifestyle and interactions with other microbes in their natural environment. Legionella pneumophila is an important human respiratory pathogen that survives and multiplies in biofilms or intracellularly within protists, such as amoebae. Importantly, transmission to humans occurs from these environmental sources. Legionella infection generally leads to rapid host cell lysis. It was therefore surprising to observe that amoebae, including fresh environmental isolates, were well protected during Legionella infection when the bacterial symbiont Protochlamydia amoebophila was also present. Legionella was not prevented from invading amoebae but was impeded in its ability to develop fully virulent progeny and were ultimately cleared in the presence of the symbiont. This study highlights how ecology and virulence of an important human pathogen is affected by a defensive amoeba symbiont, with possibly major consequences for public health. Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophila infection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila. The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.
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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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Klöckner A, Nagel M, Greub G, Aeby S, Hoffmann K, Liégeois F, Rouet F, De Benedetti S, Borel N, Henrichfreise B. Chlamydia-Related Bacteria in Free-Living and Captive Great Apes, Gabon. Emerg Infect Dis 2018; 22:2199-2201. [PMID: 27869611 PMCID: PMC5189123 DOI: 10.3201/eid2212.150893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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11
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Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont. mSystems 2017; 2:mSystems00202-16. [PMID: 28593198 PMCID: PMC5451489 DOI: 10.1128/msystems.00202-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/03/2017] [Indexed: 11/20/2022] Open
Abstract
Chlamydiae are obligate intracellular bacteria comprising well-known human pathogens and ubiquitous symbionts of protists, which are characterized by a unique developmental cycle. Here we comprehensively analyzed gene expression dynamics of Protochlamydia amoebophila during infection of its Acanthamoeba host by RNA sequencing. This revealed a highly dynamic transcriptional landscape, where major transcriptional shifts are conserved among chlamydial symbionts and pathogens. Our data served to propose a time-resolved model for type III protein secretion during the developmental cycle, and we provide evidence for a biphasic metabolism of P. amoebophila during infection, which involves energy parasitism and amino acids as the carbon source during initial stages and a postreplicative switch to endogenous glucose-based ATP production. This fits well with major transcriptional changes in the amoeba host, where upregulation of complex sugar breakdown precedes the P. amoebophila metabolic switch. The biphasic chlamydial metabolism represents a unique adaptation to exploit eukaryotic host cells, which likely contributed to the evolutionary success of this group of microbes. IMPORTANCE Chlamydiae are known as major bacterial pathogens of humans, causing the ancient disease trachoma, but they are also frequently found in the environment where they infect ubiquitous protists such as amoebae. All known chlamydiae require a eukaryotic host cell to thrive. Using the environmental chlamydia Protochlamydia amoebophila within its natural host, Acanthamoeba castellanii, we investigated gene expression dynamics in vivo and throughout the complete chlamydial developmental cycle for the first time. This allowed us to infer how a major virulence mechanism, the type III secretion system, is regulated and employed, and we show that the physiology of chlamydiae undergoes a complete shift regarding carbon metabolism and energy generation. This study provides comprehensive insights into the infection strategy of chlamydiae and reveals a unique adaptation to life within a eukaryotic host cell.
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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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13
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Pinos S, Pontarotti P, Raoult D, Merhej V. Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. BMC Evol Biol 2017; 17:75. [PMID: 28274202 PMCID: PMC5343374 DOI: 10.1186/s12862-017-0921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan. RESULTS Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats. CONCLUSIONS The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions.
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Affiliation(s)
- Sandrine Pinos
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
| | - Didier Raoult
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Vicky Merhej
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
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14
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Mehlitz A, Eylert E, Huber C, Lindner B, Vollmuth N, Karunakaran K, Goebel W, Eisenreich W, Rudel T. Metabolic adaptation ofChlamydia trachomatisto mammalian host cells. Mol Microbiol 2017; 103:1004-1019. [DOI: 10.1111/mmi.13603] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Adrian Mehlitz
- Department of Microbiology; University of Würzburg, Biocenter; Am Hubland Würzburg D-97074 Germany
| | - Eva Eylert
- Technische Universität München, Chair of Biochemistry; Lichtenbergstr. 4 Garching D-85745 Germany
| | - Claudia Huber
- Technische Universität München, Chair of Biochemistry; Lichtenbergstr. 4 Garching D-85745 Germany
| | - Buko Lindner
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Bioanalytical Chemistry; Borstel D-23845 Germany
| | - Nadine Vollmuth
- Department of Microbiology; University of Würzburg, Biocenter; Am Hubland Würzburg D-97074 Germany
| | - Karthika Karunakaran
- Department of Microbiology; University of Würzburg, Biocenter; Am Hubland Würzburg D-97074 Germany
| | - Werner Goebel
- Ludwig Maximilian University of Munich, Max von Pettenkofer-Institute; Pettenkoferstr. 9A München D-80336 Germany
| | - Wolfgang Eisenreich
- Technische Universität München, Chair of Biochemistry; Lichtenbergstr. 4 Garching D-85745 Germany
| | - Thomas Rudel
- Department of Microbiology; University of Würzburg, Biocenter; Am Hubland Würzburg D-97074 Germany
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15
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Pinos S, Pontarotti P, Raoult D, Baudoin JP, Pagnier I. Compartmentalization in PVC super-phylum: evolution and impact. Biol Direct 2016; 11:38. [PMID: 27507008 PMCID: PMC4977879 DOI: 10.1186/s13062-016-0144-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/02/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomyces and several Verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). The evolution and function of this cell plan is still subject to debate. In this work, we hypothesized that it could play a role in protection of the bacterial DNA, especially against Horizontal Genes Transfers (HGT). Therefore, 64 bacterial genomes belonging to seven different phyla (whose four PVC phyla) were studied. We reconstructed the evolution of the cell plan as precisely as possible, thanks to information obtained by bibliographic study and electronic microscopy. We used a strategy based on comparative phylogenomic in order to determine the part occupied by the horizontal transfers for each studied genomes. RESULTS Our results show that the bacteria Simkania negevensis (Chlamydiae) and Coraliomargarita akajimensis (Verrucomicrobiae), whose cell plan were unknown before, are compartmentalized, as we can see on the micrographies. This is one of the first indication of the presence of an intracytoplasmic membrane in a Chlamydiae. The proportion of HGT does not seems to be related to the cell plan of bacteria, suggesting that compartmentalization does not induce a protection of bacterial DNA against HGT. Conversely, lifestyle of bacteria seems to impact the ability of bacteria to exchange genes. CONCLUSIONS Our study allows a best reconstruction of the evolution of intracytoplasmic membrane, but this structure seems to have no impact on HGT occurrences. REVIEWERS This article was reviewed by Mircea Podar and Olivier Tenaillon.
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Affiliation(s)
- Sandrine Pinos
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 13385 Marseille, Cedex 5, France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 13385 Marseille, Cedex 5, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean Pierre Baudoin
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Isabelle Pagnier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
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16
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Cenci U, Ducatez M, Kadouche D, Colleoni C, Ball SG. Was the Chlamydial Adaptative Strategy to Tryptophan Starvation an Early Determinant of Plastid Endosymbiosis? Front Cell Infect Microbiol 2016; 6:67. [PMID: 27446814 PMCID: PMC4916741 DOI: 10.3389/fcimb.2016.00067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/07/2016] [Indexed: 12/17/2022] Open
Abstract
Chlamydiales were recently proposed to have sheltered the future cyanobacterial ancestor of plastids in a common inclusion. The intracellular pathogens are thought to have donated those critical transporters that triggered the efflux of photosynthetic carbon and the consequent onset of symbiosis. Chlamydiales are also suspected to have encoded glycogen metabolism TTS (Type Three Secretion) effectors responsible for photosynthetic carbon assimilation in the eukaryotic cytosol. We now review the reasons underlying other chlamydial lateral gene transfers evidenced in the descendants of plastid endosymbiosis. In particular we show that half of the genes encoding enzymes of tryptophan synthesis in Archaeplastida are of chlamydial origin. Tryptophan concentration is an essential cue triggering two alternative modes of replication in Chlamydiales. In addition, sophisticated tryptophan starvation mechanisms are known to act as antibacterial defenses in animal hosts. We propose that Chlamydiales have donated their tryptophan operon to the emerging plastid to ensure increased synthesis of tryptophan by the plastid ancestor. This would have allowed massive expression of the tryptophan rich chlamydial transporters responsible for symbiosis. It would also have allowed possible export of this valuable amino-acid in the inclusion of the tryptophan hungry pathogens. Free-living single cell cyanobacteria are devoid of proteins able to transport this amino-acid. We therefore investigated the phylogeny of the Tyr/Trp transporters homologous to E. coli TyrP/Mre and found yet another LGT from Chlamydiales to Archaeplastida thereby considerably strengthening our proposal.
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Affiliation(s)
- Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq France
| | - Mathieu Ducatez
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq France
| | - Derifa Kadouche
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq France
| | - Christophe Colleoni
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq France
| | - Steven G Ball
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq France
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17
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Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen. Microbiol Mol Biol Rev 2016; 80:411-27. [PMID: 27030552 DOI: 10.1128/mmbr.00071-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chlamydia species infect millions of individuals worldwide and are important etiological agents of sexually transmitted disease, infertility, and blinding trachoma. Historically, the genetic intractability of this intracellular pathogen has hindered the molecular dissection of virulence factors contributing to its pathogenesis. The obligate intracellular life cycle of Chlamydia and restrictions on the use of antibiotics as selectable markers have impeded the development of molecular tools to genetically manipulate these pathogens. However, recent developments in the field have resulted in significant gains in our ability to alter the genome of Chlamydia, which will expedite the elucidation of virulence mechanisms. In this review, we discuss the challenges affecting the development of molecular genetic tools for Chlamydia and the work that laid the foundation for recent advancements in the genetic analysis of this recalcitrant pathogen.
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18
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Pizzetti I, Schulz F, Tyml T, Fuchs BM, Amann R, Horn M, Fazi S. Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake. Environ Microbiol 2015; 18:2405-17. [PMID: 26530333 DOI: 10.1111/1462-2920.13111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 12/01/2022]
Abstract
The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.
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Affiliation(s)
- Ilaria Pizzetti
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
| | - Frederik Schulz
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Tomáš Tyml
- University of South Bohemia, Faculty of Science, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Masaryk University, Department of Botany and Zoology, Faculty of Science, Kotlářská 2, 61137, Brno, Czech Republic
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Matthias Horn
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Stefano Fazi
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
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19
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Herweg JA, Pons V, Becher D, Hecker M, Krohne G, Barbier J, Berger H, Rudel T, Mehlitz A. Proteomic analysis of the Simkania-containing vacuole: the central role of retrograde transport. Mol Microbiol 2015; 99:151-71. [PMID: 26374382 DOI: 10.1111/mmi.13222] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2015] [Indexed: 01/25/2023]
Abstract
Simkania negevensis is an obligate intracellular bacterial pathogen that grows in amoeba or human cells within a membrane-bound vacuole forming endoplasmic reticulum (ER) contact sites. The membrane of this Simkania-containing vacuole (SnCV) is a critical host-pathogen interface whose origin and molecular interactions with cellular organelles remain poorly defined. We performed proteomic analysis of purified ER-SnCV-membranes using label free LC-MS(2) to define the pathogen-containing organelle composition. Of the 1,178 proteins of human and 302 proteins of Simkania origin identified by this strategy, 51 host cell proteins were enriched or depleted by infection and 57 proteins were associated with host endosomal transport pathways. Chemical inhibitors that selectively interfere with trafficking at the early endosome-to-trans-Golgi network (TGN) interface (retrograde transport) affected SnCV formation, morphology and lipid transport. Our data demonstrate that Simkania exploits early endosome-to-TGN transport for nutrient acquisition and growth.
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Affiliation(s)
- Jo-Ana Herweg
- Department of Microbiology, University of Würzburg, Biocenter, Am Hubland, D-97074, Würzburg, Germany
| | - Valérie Pons
- DSV, iBiTec-S, LabEx LERMIT, CEA, F-91191, Gif sur Yvette, France
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Institute of Microbiology, Friedrich-Ludwig-Jahn-Straße 15, D-17487, Greifswald, Germany
| | - Michael Hecker
- Microbial Physiology/Molecular Biology, University of Greifswald, Institute of Microbiology, Friedrich-Ludwig-Jahn-Straße 15, D-17487, Greifswald, Germany
| | - Georg Krohne
- Division of Electron Microscopy, University of Würzburg, Biocenter, Am Hubland, D-97074, Würzburg, Germany
| | - Julien Barbier
- DSV, iBiTec-S, LabEx LERMIT, CEA, F-91191, Gif sur Yvette, France
| | - Hilmar Berger
- Department of Molecular Biology, Max-Planck-Institute for Infection Biology, Charitéplatz 1, D-10117, Berlin, Germany
| | - Thomas Rudel
- Department of Microbiology, University of Würzburg, Biocenter, Am Hubland, D-97074, Würzburg, Germany
| | - Adrian Mehlitz
- Department of Microbiology, University of Würzburg, Biocenter, Am Hubland, D-97074, Würzburg, Germany.,Department of Molecular Biology, Max-Planck-Institute for Infection Biology, Charitéplatz 1, D-10117, Berlin, Germany
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20
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Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors. PLoS One 2015. [PMID: 26207372 PMCID: PMC4514472 DOI: 10.1371/journal.pone.0133420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Research on the obligate intracellular bacterium Chlamydia trachomatis demands culture in cell-lines, but the adaptive process behind the in vivo to in vitro transition is not understood. We assessed the genomic and transcriptomic dynamics underlying C. trachomatis in vitro adaptation of strains representing the three disease groups (ocular, epithelial-genital and lymphogranuloma venereum) propagated in epithelial cells over multiple passages. We found genetic features potentially underlying phase variation mechanisms mediating the regulation of a lipid A biosynthesis enzyme (CT533/LpxC), and the functionality of the cytotoxin (CT166) through an ON/OFF mechanism. We detected inactivating mutations in CT713/porB, a scenario suggesting metabolic adaptation to the available carbon source. CT135 was inactivated in a tropism-specific manner, with CT135-negative clones emerging for all epithelial-genital populations (but not for LGV and ocular populations) and rapidly increasing in frequency (~23% mutants per 10 passages). RNA-sequencing analyses revealed that a deletion event involving CT135 impacted the expression of multiple virulence factors, namely effectors known to play a role in the C. trachomatis host-cell invasion or subversion (e.g., CT456/Tarp, CT694, CT875/TepP and CT868/ChlaDub1). This reflects a scenario of attenuation of C. trachomatis virulence in vitro, which may take place independently or in a cumulative fashion with the also observed down-regulation of plasmid-related virulence factors. This issue may be relevant on behalf of the recent advances in Chlamydia mutagenesis and transformation where culture propagation for selecting mutants/transformants is mandatory. Finally, there was an increase in the growth rate for all strains, reflecting gradual fitness enhancement over time. In general, these data shed light on the adaptive process underlying the C. trachomatis in vivo to in vitro transition, and indicates that it would be prudent to restrict culture propagation to minimal passages and check the status of the CT135 genotype in order to avoid the selection of CT135-negative mutants, likely originating less virulent strains.
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21
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Domman D, Horn M, Embley TM, Williams TA. Plastid establishment did not require a chlamydial partner. Nat Commun 2015; 6:6421. [PMID: 25758953 PMCID: PMC4374161 DOI: 10.1038/ncomms7421] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/27/2015] [Indexed: 12/28/2022] Open
Abstract
Primary plastids descend from the cyanobacterial endosymbiont of an ancient eukaryotic host, but the initial selective drivers that stabilized the association between these two cells are still unclear. One hypothesis that has achieved recent prominence suggests that the first role of the cyanobiont was in energy provision for a host cell whose reserves were being depleted by an intracellular chlamydial pathogen. A pivotal claim is that it was chlamydial proteins themselves that converted otherwise unusable cyanobacterial metabolites into host energy stores. We test this hypothesis by investigating the origins of the key enzymes using sophisticated phylogenetics. Here we show a mosaic origin for the relevant pathway combining genes with host, cyanobacterial or bacterial ancestry, but we detect no strong case for Chlamydiae to host transfer under the best-fitting models. Our conclusion is that there is no compelling evidence from gene trees that Chlamydiae played any role in establishing the primary plastid endosymbiosis. Primary plastids descend from an endosymbiosis involving cyanobacteria, an ancient eukaryotic host and, possibly, a chlamydial pathogen. Here, Domman and colleagues use sophisticated phylogenetic methods to show that Chlamydiae did not play a role in establishing the primary plastid endosymbiosis.
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Affiliation(s)
- Daryl Domman
- Department of Microbiology and Ecosystem Science, University of Vienna, A-1090 Vienna, Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, University of Vienna, A-1090 Vienna, Austria
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tom A Williams
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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22
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Sachse K, Bavoil PM, Kaltenboeck B, Stephens RS, Kuo CC, Rosselló-Móra R, Horn M. Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species. Syst Appl Microbiol 2015; 38:99-103. [PMID: 25618261 DOI: 10.1016/j.syapm.2014.12.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/22/2014] [Accepted: 12/27/2014] [Indexed: 01/29/2023]
Abstract
The family Chlamydiaceae (order Chlamydiales, phylum Chlamydiae) comprises important, obligate intracellular bacterial pathogens of humans and animals. Subdivision of the family into the two genera Chlamydia and Chlamydophila has been discussed controversially during the past decade. Here, we have revisited the current classification in the light of recent genomic data and in the context of the unique biological properties of these microorganisms. We conclude that neither generally used 16S rRNA sequence identity cut-off values nor parameters based on genomic similarity consistently separate the two genera. Notably, no easily recognizable phenotype such as host preference or tissue tropism is available that would support a subdivision. In addition, the genus Chlamydophila is currently not well accepted and not used by a majority of research groups in the field. Therefore, we propose the classification of all 11 currently recognized Chlamydiaceae species in a single genus, the genus Chlamydia. Finally, we provide emended descriptions of the family Chlamydiaceae, the genus Chlamydia, as well as the species Chlamydia abortus, Chlamydia caviae and Chlamydia felis.
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Affiliation(s)
- Konrad Sachse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany.
| | - Patrik M Bavoil
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA
| | - Bernhard Kaltenboeck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Richard S Stephens
- Program in Infectious Diseases, University of California, Berkeley, CA, USA
| | | | - Ramon Rosselló-Móra
- Mediterranean Institute for Advanced studies (IMEDEA, CSIC-UIB), Esporles, Illes Balears, Spain
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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23
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Knie N, Polsakiewicz M, Knoop V. Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria. Mol Biol Evol 2014; 32:629-34. [PMID: 25415968 DOI: 10.1093/molbev/msu324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.
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Affiliation(s)
- Nils Knie
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Monika Polsakiewicz
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
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24
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Zimorski V, Ku C, Martin WF, Gould SB. Endosymbiotic theory for organelle origins. Curr Opin Microbiol 2014; 22:38-48. [PMID: 25306530 DOI: 10.1016/j.mib.2014.09.008] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/01/2014] [Accepted: 09/12/2014] [Indexed: 11/19/2022]
Abstract
Endosymbiotic theory goes back over 100 years. It explains the similarity of chloroplasts and mitochondria to free-living prokaryotes by suggesting that the organelles arose from prokaryotes through (endo)symbiosis. Gene trees provide important evidence in favour of symbiotic theory at a coarse-grained level, but the finer we get into the details of branches in trees containing dozens or hundreds of taxa, the more equivocal evidence for endosymbiotic events sometimes becomes. It seems that either the interpretation of some endosymbiotic events are wrong, or something is wrong with the interpretations of some gene trees having many leaves. There is a need for evidence that is independent of gene trees and that can help outline the course of symbiosis in eukaryote evolution. Protein import is the strongest evidence we have for the single origin of chloroplasts and mitochondria. It is probably also the strongest evidence we have to sort out the number and nature of secondary endosymbiotic events that have occurred in evolution involving the red plastid lineage. If we relax our interpretation of individual gene trees, endosymbiotic theory can tell us a lot.
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Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine-University of Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University of Düsseldorf, 40225 Düsseldorf, Germany.
| | - Sven B Gould
- Institute of Molecular Evolution, Heinrich-Heine-University of Düsseldorf, 40225 Düsseldorf, Germany
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25
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Domman D, Collingro A, Lagkouvardos I, Gehre L, Weinmaier T, Rattei T, Subtil A, Horn M. Massive expansion of Ubiquitination-related gene families within the Chlamydiae. Mol Biol Evol 2014; 31:2890-904. [PMID: 25069652 PMCID: PMC4209131 DOI: 10.1093/molbev/msu227] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. Despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum Chlamydiae revealed that within the family Parachlamydiaceae, gene family expansions have had pronounced effects on gene content. We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution. These large gene families are comprised of members harboring eukaryotic-like ubiquitination-related domains, such as F-box and BTB-box domains, marking the largest reservoir of these proteins found among bacteria. A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell. The large disparity in copy number of members in these families between closely related organisms suggests that nonadaptive processes might contribute to the evolution of these gene families. Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.
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Affiliation(s)
- Daryl Domman
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Astrid Collingro
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ilias Lagkouvardos
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Lena Gehre
- Unité de Biologie des Interactions Cellulaires, Institut Pasteur, Paris, France
| | - Thomas Weinmaier
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Agathe Subtil
- Unité de Biologie des Interactions Cellulaires, Institut Pasteur, Paris, France
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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26
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Pilhofer M, Aistleitner K, Ladinsky MS, König L, Horn M, Jensen GJ. Architecture and host interface of environmental chlamydiae revealed by electron cryotomography. Environ Microbiol 2013; 16:417-29. [PMID: 24118768 PMCID: PMC4949044 DOI: 10.1111/1462-2920.12299] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/26/2013] [Indexed: 01/14/2023]
Abstract
Chlamydiae comprise important pathogenic and symbiotic bacteria that alternate between morphologically and physiologically different life stages during their developmental cycle. Using electron cryotomography, we characterize the ultrastructure of the developmental stages of three environmental chlamydiae: Parachlamydia acanthamoebae, Protochlamydia amoebophila and Simkania negevensis. We show that chemical fixation and dehydration alter the cell shape of Parachlamydia and that the crescent body is not a developmental stage, but an artefact of conventional electron microscopy. We further reveal type III secretion systems of environmental chlamydiae at macromolecular resolution and find support for a chlamydial needle-tip protein. Imaging bacteria inside their host cells by cryotomography for the first time, we observe marked differences in inclusion morphology and development as well as host organelle recruitment between the three chlamydial organisms, with Simkania inclusions being tightly enveloped by the host endoplasmic reticulum. The study demonstrates the power of electron cryotomography to reveal structural details of bacteria-host interactions that are not accessible using traditional methods.
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Affiliation(s)
- Martin Pilhofer
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA; Howard Hughes Medical Institute, Pasadena, CA, 91125, USA
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