Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae

Abstract

Gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. Despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum Chlamydiae revealed that within the family Parachlamydiaceae, gene family expansions have had pronounced effects on gene content. We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution. These large gene families are comprised of members harboring eukaryotic-like ubiquitination-related domains, such as F-box and BTB-box domains, marking the largest reservoir of these proteins found among bacteria. A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell. The large disparity in copy number of members in these families between closely related organisms suggests that nonadaptive processes might contribute to the evolution of these gene families. Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.

Orientia tsutsugamushi Strain Ikeda Ankyrin Repeat-Containing Proteins Recruit SCF1 Ubiquitin Ligase Machinery via Poxvirus-Like F-Box Motifs

“…(22,32,33). C. burnetii encodes three F-box-containing proteins, one of which, CpeC, is secreted into host cells and colocalizes with ubiquitin-rich structures (37), though its specific function is not yet known.…”

“…Of the bacterial F-box proteins described thus far, most have their F-boxes N-terminally located with additional protein-protein interaction domains downstream, similar to the arrangement of eukaryotic F-box proteins (22,32,33). One exception is GogB, which has a C-terminal F-box positioned downstream from a non-ankyrin repeat domain (36).…”

“…As the final SCF1 component, the FBP interacts with the target protein via its protein-protein interaction domain, acting as a substrate specificity module to direct SCF1-mediated polyubiquitination of the target (29,30). Numerous intracellular bacterial pathogens encode FBPs (20)(21)(22)(31)(32)(33)(34)(35)(36)(37), evidencing their potential to exploit the SCF1 complex.…”

CRISPR system acquisition and evolution of an obligate intracellularChlamydia-related bacterium

“…Although a confirmed CRISPR locus was predicted by CRISPRfinder (Grissa et al 2007) in the recently released genomes of Neochlamydia sp. (Domman et al 2014;Ishida et al 2014), no cas genes could be identified and the repeats were found to be due to a highly repeated protein sequence.…”

CRISPR System Acquisition and Evolution of an Obligate IntracellularChlamydia-Related Bacterium

“…On the contrary, the occurrence of large families of paralogs in the genome of various families within the order Chlamydiales , and particularly in Parachlamydiaceae , suggested evolution by extensive gene duplication (Eugster et al 2007; Domman et al 2014). The chromosome sequence of Pr.…”