Unity in variety-the pan-genome of the chlamydiae

Collingro, A; Tischler, P; Weinmaier, T; Penz, T; Heinz, E; Brunham, RC; Read, TD; Bavoil, PM; Sachse, K; Kahane, S; Friedman, MG; Rattei, T; Myers, GSA; Horn, M

Unity in variety-the pan-genome of the chlamydiae

Collingro, A Tischler, P Weinmaier, T Penz, T Heinz, E Brunham, RC Read, TD Bavoil, PM Sachse, K Kahane, S Friedman, MG Rattei, T Myers, GSA

Horn, M

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Publication Type:: Journal Article
Citation:: Molecular Biology and Evolution, 2011, 28 (12), pp. 3253 - 3270
Issue Date:: 2011-12-01

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Field	Value	Language
dc.contributor.author	Collingro, A	en_US
dc.contributor.author	Tischler, P	en_US
dc.contributor.author	Weinmaier, T	en_US
dc.contributor.author	Penz, T	en_US
dc.contributor.author	Heinz, E	en_US
dc.contributor.author	Brunham, RC	en_US
dc.contributor.author	Read, TD	en_US
dc.contributor.author	Bavoil, PM	en_US
dc.contributor.author	Sachse, K	en_US
dc.contributor.author	Kahane, S	en_US
dc.contributor.author	Friedman, MG	en_US
dc.contributor.author	Rattei, T	en_US
dc.contributor.author	Myers, GSA https://orcid.org/0000-0002-4756-4810	en_US
dc.contributor.author	Horn, M	en_US
dc.date.issued	2011-12-01	en_US
dc.identifier.citation	Molecular Biology and Evolution, 2011, 28 (12), pp. 3253 - 3270	en_US
dc.identifier.issn	0737-4038	en_US
dc.identifier.uri	http://hdl.handle.net/10453/39734
dc.description.abstract	Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote. © 2011 The Author.	en_US
dc.relation.ispartof	Molecular Biology and Evolution	en_US
dc.relation.isbasedon	10.1093/molbev/msr161	en_US
dc.subject.classification	Evolutionary Biology	en_US
dc.subject.mesh	Cell Membrane	en_US
dc.subject.mesh	Chlamydiales	en_US
dc.subject.mesh	Chlamydia	en_US
dc.subject.mesh	Bacterial Proteins	en_US
dc.subject.mesh	Bacterial Outer Membrane Proteins	en_US
dc.subject.mesh	DNA, Bacterial	en_US
dc.subject.mesh	RNA, Ribosomal, 16S	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Evolution, Molecular	en_US
dc.subject.mesh	Phylogeny	en_US
dc.subject.mesh	Symbiosis	en_US
dc.subject.mesh	Gene Transfer, Horizontal	en_US
dc.subject.mesh	Base Sequence	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Plasmids	en_US
dc.subject.mesh	Molecular Sequence Data	en_US
dc.subject.mesh	Host-Pathogen Interactions	en_US
dc.subject.mesh	Genetic Variation	en_US
dc.subject.mesh	Bacterial Secretion Systems	en_US
dc.title	Unity in variety-the pan-genome of the chlamydiae	en_US
dc.type	Journal Article
utslib.citation.volume	12	en_US
utslib.citation.volume	28	en_US
utslib.for	0601 Biochemistry and Cell Biology	en_US
utslib.for	0603 Evolutionary Biology	en_US
utslib.for	0604 Genetics	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	closed_access
pubs.issue	12	en_US
pubs.publication-status	Published	en_US
pubs.volume	28	en_US

Abstract:

Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote. © 2011 The Author.

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http://hdl.handle.net/10453/39734