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Massive expansion of Ubiquitination-related gene families within the Chlamydiae.

Domman D, Collingro A, Lagkouvardos I, Gehre L, Weinmaier T, Rattei T, Subtil A, Horn M - Mol. Biol. Evol. (2014)

Bottom Line: We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution.A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell.Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.

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Phylogeny of the Chlamydiae and rearrangement history of genomes within the Parachlamydiaceae. Phylogeny of the Chlamydiae based on 32 phylogenetic marker proteins. A Bayesian analysis using MrBayes (Ronquist and Huelsenbeck 2003) was performed on a set of 24 ribosomal proteins in addition to GyrB, RecA, RpoB, RpoC, and EF-Tu from 19 sequenced members of the phylum (supplementary table S2, Supplementary Material online). Members of the Planctomycetes (Blastopirellula marina DSM 3645, Candidatus Kuenenia stuttgartiensis, and Gemmata obscuriglobus UQM 2246) and the Verrucomicrobia (Akkermansia muciniphila MucT, Lentisphaera araneosa HTCC2155, Opitutus terrae PB90-1, and Verrucomicrobium spinosum DSM 4136) were used as outgroups (not shown). Colors denote family level classification. Posterior probability scores are indicated only if below 100%. To the right, conserved synteny and rearrangement history of genomes within the Parachlamydiaceae are shown. The genomes of six members of the family were aligned using MAUVE to elucidate synteny between genomes and visualized using genoPlotR. Extensive rearrangements are apparent between members of different genera, whereas within genus, comparisons show little rearrangements, with a notable exception in the Protochlamydia where a large block has been rearranged.
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msu227-F1: Phylogeny of the Chlamydiae and rearrangement history of genomes within the Parachlamydiaceae. Phylogeny of the Chlamydiae based on 32 phylogenetic marker proteins. A Bayesian analysis using MrBayes (Ronquist and Huelsenbeck 2003) was performed on a set of 24 ribosomal proteins in addition to GyrB, RecA, RpoB, RpoC, and EF-Tu from 19 sequenced members of the phylum (supplementary table S2, Supplementary Material online). Members of the Planctomycetes (Blastopirellula marina DSM 3645, Candidatus Kuenenia stuttgartiensis, and Gemmata obscuriglobus UQM 2246) and the Verrucomicrobia (Akkermansia muciniphila MucT, Lentisphaera araneosa HTCC2155, Opitutus terrae PB90-1, and Verrucomicrobium spinosum DSM 4136) were used as outgroups (not shown). Colors denote family level classification. Posterior probability scores are indicated only if below 100%. To the right, conserved synteny and rearrangement history of genomes within the Parachlamydiaceae are shown. The genomes of six members of the family were aligned using MAUVE to elucidate synteny between genomes and visualized using genoPlotR. Extensive rearrangements are apparent between members of different genera, whereas within genus, comparisons show little rearrangements, with a notable exception in the Protochlamydia where a large block has been rearranged.

Mentions: Currently, there are nine described families within the Chlamydiae; however, the majority of available genome sequences come from a single family, the pathogenic Chlamydiaceae. To deepen our insights into a family outside of the Chlamydiaceae, we sequenced the genomes of four members of the family Parachlamydiaceae, which include two members of the genus Neochlamydia, and two additional genomes of Protochlamydia and Parachlamydia. All of the newly sequenced Parachlamydiaceae members were isolated from free-living amoeba. With the exception of Neochlamydia sp. EPS4, the isolates have been described previously (Fritsche et al. 2000; Heinz et al. 2007; Schmitz-Esser et al. 2008). The draft genomes represent nearly complete genome sequences based on paired end read data (90–96%) and the presence of conserved single-copy marker genes (98–100%; supplementary table S1, Supplementary Material online). Using these additional genome sequences, we first aimed to construct a phylogenetic framework of the phylum Chlamydiae using concatenated alignments of 32 marker proteins (supplementary table S2, Supplementary Material online). Phylogenetic trees obtained with different methods confirmed the monophyly of the Chlamydiaceae and the Parachlamydiaceae with strong support (fig. 1). The Chlamydiaceae can be subdivided in two previously recognized groups, and within the Parachlamydiaceae, the genera Protochlamydia, Neochlamydia, and Parachlamydia were recovered with high confidence.Fig. 1.


Massive expansion of Ubiquitination-related gene families within the Chlamydiae.

Domman D, Collingro A, Lagkouvardos I, Gehre L, Weinmaier T, Rattei T, Subtil A, Horn M - Mol. Biol. Evol. (2014)

Phylogeny of the Chlamydiae and rearrangement history of genomes within the Parachlamydiaceae. Phylogeny of the Chlamydiae based on 32 phylogenetic marker proteins. A Bayesian analysis using MrBayes (Ronquist and Huelsenbeck 2003) was performed on a set of 24 ribosomal proteins in addition to GyrB, RecA, RpoB, RpoC, and EF-Tu from 19 sequenced members of the phylum (supplementary table S2, Supplementary Material online). Members of the Planctomycetes (Blastopirellula marina DSM 3645, Candidatus Kuenenia stuttgartiensis, and Gemmata obscuriglobus UQM 2246) and the Verrucomicrobia (Akkermansia muciniphila MucT, Lentisphaera araneosa HTCC2155, Opitutus terrae PB90-1, and Verrucomicrobium spinosum DSM 4136) were used as outgroups (not shown). Colors denote family level classification. Posterior probability scores are indicated only if below 100%. To the right, conserved synteny and rearrangement history of genomes within the Parachlamydiaceae are shown. The genomes of six members of the family were aligned using MAUVE to elucidate synteny between genomes and visualized using genoPlotR. Extensive rearrangements are apparent between members of different genera, whereas within genus, comparisons show little rearrangements, with a notable exception in the Protochlamydia where a large block has been rearranged.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4209131&req=5

msu227-F1: Phylogeny of the Chlamydiae and rearrangement history of genomes within the Parachlamydiaceae. Phylogeny of the Chlamydiae based on 32 phylogenetic marker proteins. A Bayesian analysis using MrBayes (Ronquist and Huelsenbeck 2003) was performed on a set of 24 ribosomal proteins in addition to GyrB, RecA, RpoB, RpoC, and EF-Tu from 19 sequenced members of the phylum (supplementary table S2, Supplementary Material online). Members of the Planctomycetes (Blastopirellula marina DSM 3645, Candidatus Kuenenia stuttgartiensis, and Gemmata obscuriglobus UQM 2246) and the Verrucomicrobia (Akkermansia muciniphila MucT, Lentisphaera araneosa HTCC2155, Opitutus terrae PB90-1, and Verrucomicrobium spinosum DSM 4136) were used as outgroups (not shown). Colors denote family level classification. Posterior probability scores are indicated only if below 100%. To the right, conserved synteny and rearrangement history of genomes within the Parachlamydiaceae are shown. The genomes of six members of the family were aligned using MAUVE to elucidate synteny between genomes and visualized using genoPlotR. Extensive rearrangements are apparent between members of different genera, whereas within genus, comparisons show little rearrangements, with a notable exception in the Protochlamydia where a large block has been rearranged.
Mentions: Currently, there are nine described families within the Chlamydiae; however, the majority of available genome sequences come from a single family, the pathogenic Chlamydiaceae. To deepen our insights into a family outside of the Chlamydiaceae, we sequenced the genomes of four members of the family Parachlamydiaceae, which include two members of the genus Neochlamydia, and two additional genomes of Protochlamydia and Parachlamydia. All of the newly sequenced Parachlamydiaceae members were isolated from free-living amoeba. With the exception of Neochlamydia sp. EPS4, the isolates have been described previously (Fritsche et al. 2000; Heinz et al. 2007; Schmitz-Esser et al. 2008). The draft genomes represent nearly complete genome sequences based on paired end read data (90–96%) and the presence of conserved single-copy marker genes (98–100%; supplementary table S1, Supplementary Material online). Using these additional genome sequences, we first aimed to construct a phylogenetic framework of the phylum Chlamydiae using concatenated alignments of 32 marker proteins (supplementary table S2, Supplementary Material online). Phylogenetic trees obtained with different methods confirmed the monophyly of the Chlamydiaceae and the Parachlamydiaceae with strong support (fig. 1). The Chlamydiaceae can be subdivided in two previously recognized groups, and within the Parachlamydiaceae, the genera Protochlamydia, Neochlamydia, and Parachlamydia were recovered with high confidence.Fig. 1.

Bottom Line: We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution.A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell.Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.

Show MeSH
Related in: MedlinePlus