title: 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.
authors: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors: Daryl
authors: D
authors: Domman
authors: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors: Astrid
authors: A
authors: Collingro
authors: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors: Ilias
authors: I
authors: Lagkouvardos
authors: Unité de Biologie des Interactions Cellulaires, Institut Pasteur, Paris, France.
authors: Lena
authors: L
authors: Gehre
authors: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors: Thomas
authors: T
authors: Weinmaier
authors: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors: Thomas
authors: T
authors: Rattei
authors: Unité de Biologie des Interactions Cellulaires, Institut Pasteur, Paris, France.
authors: Agathe
authors: A
authors: Subtil
authors: Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria horn@microbial-ecology.net.
authors: Matthias
authors: M
authors: Horn
mesh_terms: D058947:Bacterial Secretion Systems / Q000235:genetics*; D002693:Chlamydiaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D018628:Gene Dosage; D014644:Genetic Variation; D016680:Genome, Bacterial; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D054875:Ubiquitination / Q000235:genetics*
chemical_list: D058947:Bacterial Secretion Systems
keywords: F-box; birth and death model; effector proteins; gene families; intracellular bacteria