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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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Protein domain architecture of largest gene families. The domain architecture of Neochlamydia (NEX1, NEX2) and Protochlamydia (PEX1, PEX2) gene families are shown. The range of the number of domain repeats and functional assignments of the detected domains are indicated. NEX1 can be divided into two subfamilies based on phylogeny and domain presence/absence. A role of these proteins in the context of eukaryotic cells can be postulated based on the presence of domains otherwise found in eukaryotes.
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msu227-F3: Protein domain architecture of largest gene families. The domain architecture of Neochlamydia (NEX1, NEX2) and Protochlamydia (PEX1, PEX2) gene families are shown. The range of the number of domain repeats and functional assignments of the detected domains are indicated. NEX1 can be divided into two subfamilies based on phylogeny and domain presence/absence. A role of these proteins in the context of eukaryotic cells can be postulated based on the presence of domains otherwise found in eukaryotes.

Mentions: The largest gene family, termed Neochlamydia expansion 1 (NEX1), in the phylum comprised a total of 138 members, which are contributed by the two Neochlamydia genomes. The domain architecture within this large gene family is heterogeneous; however, all proteins contain various C-terminal repetitions of LRR domains (fig. 3). We have identified two subfamilies that we delineate NEX1a and NEX1b within the NEX1 family. The majority of members fall into the NEX1a subfamily, in which they have a highly conserved N-terminal F-box or F-box-like domain. The members have an average of 77% sequence similarity among each other, and the F-box-like domain is 57% and 45% similar to Acanthamoeba castellanii and human F-box-like domains, respectively. The smaller NEX1b family, in contrast, has a conserved RING/U-box at the N-terminus. Both the F-box and RING/U-box domains are associated with eukaryotic E3 ubiquitin ligase complexes (Willems et al. 2004). Between all members in the NEX1 family, there is a region of roughly 50 amino acids between the predicted N-terminal domains and the LRRs that is highly conserved. However, we failed to detect any known domains in this region nor was there any homology to known proteins.Fig. 3.


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)

Protein domain architecture of largest gene families. The domain architecture of Neochlamydia (NEX1, NEX2) and Protochlamydia (PEX1, PEX2) gene families are shown. The range of the number of domain repeats and functional assignments of the detected domains are indicated. NEX1 can be divided into two subfamilies based on phylogeny and domain presence/absence. A role of these proteins in the context of eukaryotic cells can be postulated based on the presence of domains otherwise found in eukaryotes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

msu227-F3: Protein domain architecture of largest gene families. The domain architecture of Neochlamydia (NEX1, NEX2) and Protochlamydia (PEX1, PEX2) gene families are shown. The range of the number of domain repeats and functional assignments of the detected domains are indicated. NEX1 can be divided into two subfamilies based on phylogeny and domain presence/absence. A role of these proteins in the context of eukaryotic cells can be postulated based on the presence of domains otherwise found in eukaryotes.
Mentions: The largest gene family, termed Neochlamydia expansion 1 (NEX1), in the phylum comprised a total of 138 members, which are contributed by the two Neochlamydia genomes. The domain architecture within this large gene family is heterogeneous; however, all proteins contain various C-terminal repetitions of LRR domains (fig. 3). We have identified two subfamilies that we delineate NEX1a and NEX1b within the NEX1 family. The majority of members fall into the NEX1a subfamily, in which they have a highly conserved N-terminal F-box or F-box-like domain. The members have an average of 77% sequence similarity among each other, and the F-box-like domain is 57% and 45% similar to Acanthamoeba castellanii and human F-box-like domains, respectively. The smaller NEX1b family, in contrast, has a conserved RING/U-box at the N-terminus. Both the F-box and RING/U-box domains are associated with eukaryotic E3 ubiquitin ligase complexes (Willems et al. 2004). Between all members in the NEX1 family, there is a region of roughly 50 amino acids between the predicted N-terminal domains and the LRRs that is highly conserved. However, we failed to detect any known domains in this region nor was there any homology to known proteins.Fig. 3.

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