Massive expansion of Ubiquitination-related gene families within the Chlamydiae.
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.
Affiliation: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.Show MeSH
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Mentions: Driven by the discovery that members of the four largest Parachlamydiaceae gene families showed rapid divergence and are kept in chlamydial genomes despite apparent functional redundancy, we asked whether there are additional genes not included in these gene families but encoding similar functional domains. The common theme of the large Parachlamydiaceae gene families is the presence of domains that serve in the recruitment of target proteins to the eukaryotic ubiquitination machinery. We therefore extracted all proteins containing F-box/F-box-like, BTB/POZ, and RING/U-box domains by scanning all chlamydial proteomes with each respective HMM profile. We found no RING/U-box containing proteins apart from those identified earlier as members of NEX1b, and we detected only few additional proteins in Neochlamydia and Parachlamydia harboring a BTB/POZ domain similar to those of PEX1. However, our search unveiled an astonishing number of proteins harboring F-box/F-box-like domains, with over 370 proteins within the phylum. Nearly 300 of the F-box proteins are the contribution of the two Neochlamydia species (129 in TUME1 and 158 in EPS4). To characterize the relationships among this F-box superfamily, we constructed a phylogenetic tree based on a domain alignment. This analysis shows that many of the additional F-box proteins found in Neochlamydia cluster with either NEX1a or NEX2 (fig. 5a). We also see several lineage-specific expansions of F-box proteins within Protochlamydia and Parachlamydia species. Reconciliation of the F-box superfamily tree with the chlamydial species tree confirms an extremely dynamic history of large-scale gene birth and death events (fig. 5b), mirroring the evolutionary pattern seen for the large Parachlamydiaceae gene families (supplementary figs. S2–S6 and table S3, Supplementary Material online).Fig. 5.
Affiliation: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.