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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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Taxonomic profile of F-box and BTB domains. The distribution of (A) the F-box clan, and (B) the BTB-box throughout sequenced organisms. The size of the node indicates the number of species harboring proteins with the domain. Thus, larger node size indicates a larger number of species in which a domain is found within a taxon. Nodes are ordered from least to greatest by the total number of proteins that contain the domain within the taxon. This is different than the number of species as one species can have many proteins harboring a given domain. To reflect this disparity and to facilitate comparisons, we computed a normalized value for each taxon that represents the number of total proteins divided by the number of species. This normalization value is represented by the width of the arc in the diagram. For instance, the chlamydiae are represented by few species (small node size) but are among the taxa containing the largest numbers of proteins with F-Box and BTB domains (position on vertical axis) and show a high number of proteins with these domains per species (arc width). All bacterial taxa are plotted in purple and selected major eukaryotic taxa in blue. The Chlamydiae are labeled in red, and double-stranded DNA viruses are shown in green. The data were obtained from the Pfam database for each domain, and counts were updated to reflect findings in this study.
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msu227-F6: Taxonomic profile of F-box and BTB domains. The distribution of (A) the F-box clan, and (B) the BTB-box throughout sequenced organisms. The size of the node indicates the number of species harboring proteins with the domain. Thus, larger node size indicates a larger number of species in which a domain is found within a taxon. Nodes are ordered from least to greatest by the total number of proteins that contain the domain within the taxon. This is different than the number of species as one species can have many proteins harboring a given domain. To reflect this disparity and to facilitate comparisons, we computed a normalized value for each taxon that represents the number of total proteins divided by the number of species. This normalization value is represented by the width of the arc in the diagram. For instance, the chlamydiae are represented by few species (small node size) but are among the taxa containing the largest numbers of proteins with F-Box and BTB domains (position on vertical axis) and show a high number of proteins with these domains per species (arc width). All bacterial taxa are plotted in purple and selected major eukaryotic taxa in blue. The Chlamydiae are labeled in red, and double-stranded DNA viruses are shown in green. The data were obtained from the Pfam database for each domain, and counts were updated to reflect findings in this study.

Mentions: To gain a broader overview of the occurrence of F-box/F-box-like and BTB/POZ domains among other prokaryotes and eukaryotes, we extracted domain abundance data from Pfam (Finn et al. 2013) and included the current counts for the Chlamydiae genomes present in this study (fig. 6). This revealed a striking pattern that the few bacterial groups encoding proteins with F-box and BTB domains are almost exclusively amoeba-associated organisms. These include members of the Legionellales (Gammaproteobacteria), the Rickettsiales (Alphaproteobacteria), and the amoeba symbiont Amoebophilus asiaticus (Bacteroidetes). When the number of F-box proteins is normalized against the total number of species in a given taxon, the Chlamydiae lead in the number of F-box proteins found in bacteria and even harbor more than several lineages of eukaryotes including the Amoebozoa. For the BTB proteins, the Chlamydiae appear to be the only bacterial lineage that harbors this domain. It is intriguing that many of the large double-stranded DNA viruses, namely the amoeba-infecting giant viruses, contain many proteins with an F-box or BTB domain.Fig. 6.


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)

Taxonomic profile of F-box and BTB domains. The distribution of (A) the F-box clan, and (B) the BTB-box throughout sequenced organisms. The size of the node indicates the number of species harboring proteins with the domain. Thus, larger node size indicates a larger number of species in which a domain is found within a taxon. Nodes are ordered from least to greatest by the total number of proteins that contain the domain within the taxon. This is different than the number of species as one species can have many proteins harboring a given domain. To reflect this disparity and to facilitate comparisons, we computed a normalized value for each taxon that represents the number of total proteins divided by the number of species. This normalization value is represented by the width of the arc in the diagram. For instance, the chlamydiae are represented by few species (small node size) but are among the taxa containing the largest numbers of proteins with F-Box and BTB domains (position on vertical axis) and show a high number of proteins with these domains per species (arc width). All bacterial taxa are plotted in purple and selected major eukaryotic taxa in blue. The Chlamydiae are labeled in red, and double-stranded DNA viruses are shown in green. The data were obtained from the Pfam database for each domain, and counts were updated to reflect findings in this study.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4209131&req=5

msu227-F6: Taxonomic profile of F-box and BTB domains. The distribution of (A) the F-box clan, and (B) the BTB-box throughout sequenced organisms. The size of the node indicates the number of species harboring proteins with the domain. Thus, larger node size indicates a larger number of species in which a domain is found within a taxon. Nodes are ordered from least to greatest by the total number of proteins that contain the domain within the taxon. This is different than the number of species as one species can have many proteins harboring a given domain. To reflect this disparity and to facilitate comparisons, we computed a normalized value for each taxon that represents the number of total proteins divided by the number of species. This normalization value is represented by the width of the arc in the diagram. For instance, the chlamydiae are represented by few species (small node size) but are among the taxa containing the largest numbers of proteins with F-Box and BTB domains (position on vertical axis) and show a high number of proteins with these domains per species (arc width). All bacterial taxa are plotted in purple and selected major eukaryotic taxa in blue. The Chlamydiae are labeled in red, and double-stranded DNA viruses are shown in green. The data were obtained from the Pfam database for each domain, and counts were updated to reflect findings in this study.
Mentions: To gain a broader overview of the occurrence of F-box/F-box-like and BTB/POZ domains among other prokaryotes and eukaryotes, we extracted domain abundance data from Pfam (Finn et al. 2013) and included the current counts for the Chlamydiae genomes present in this study (fig. 6). This revealed a striking pattern that the few bacterial groups encoding proteins with F-box and BTB domains are almost exclusively amoeba-associated organisms. These include members of the Legionellales (Gammaproteobacteria), the Rickettsiales (Alphaproteobacteria), and the amoeba symbiont Amoebophilus asiaticus (Bacteroidetes). When the number of F-box proteins is normalized against the total number of species in a given taxon, the Chlamydiae lead in the number of F-box proteins found in bacteria and even harbor more than several lineages of eukaryotes including the Amoebozoa. For the BTB proteins, the Chlamydiae appear to be the only bacterial lineage that harbors this domain. It is intriguing that many of the large double-stranded DNA viruses, namely the amoeba-infecting giant viruses, contain many proteins with an F-box or BTB domain.Fig. 6.

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