Genomics and molecular evolution of the Planctomycetes, Verrucomicrobia, Chlamydiae super-phylum

The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum is an emerging model bacterial group for studying the evolution of biological complexity because PVC bacteria possess extensive intracellular membranes of unknown function and evolutionary origin. The cell plan of Gemmata obscuriglobus, in particular, is argued to be analogous to the early evolutionary stages of cell compartmentalization in eukaryotes. The organisms of the super-phylum also have different life-styles ranging from free-living to obligate pathogens, providing an opportunity to study the evolutionary basis of life-style shifts. Our interest in multiple aspects of PVC super-phylum biology stimulated comprehensive comparative genomic analysis of these bacteria, as described below.;We examined patterns of natural selection in different protein-coding genes within PVC bacteria, in order to identify genes potentially underlying the emergence of novel phenotypes. This work required development and application of a novel computational framework to quantify selective constraints on indel substitutions (use of dN/dS methods was not permitted due to saturation of synonymous sites). We found that indels in full-length proteins have accumulated faster than would be expected under neutrality on about 12% of evaluated gene tree branches, over all the examined gene trees. This is consistent with positive Darwinian selection acting on indels. Mapping genes with accelerated indel rates onto predicted biological functions, we revealed several trends. For instance, insertions in a-helices appeared to be affecting a large proportion of ribosomal proteins. This finding suggests interesting avenues for future experimental work, given the known partition of the PVC cell cytoplasm into ribosome-containing and ribosome-free regions, and the apparent segregation of G. obscuriglobus ribosomes from the nucleoid.;The second major study explored how events of genome content evolution (HGT, gene duplication, and loss) have affected the PVC super-phylum, through analysis of gene families reconstructed for PVC genomes and a number of out-group species. We showed that evolutionary processes contributing to genome expansion have been accelerated and decelerated within Planctomycetes and Chlamydiae, respectively, and have balanced each other in Verrucomicrobia and Lentisphaerae. These processes were inferred through Bayesian modeling of event rates (in either a simple or mixture modeling framework). It also appeared that a large number of genes were acquired on various PVC lineages from phylum Acidobacteria, and from phylum Bacteroidetes on the lineage leading to Akkermansia muciniphila, an intestinal human commensal. In the last part of this study, we identified a highly conserved genetic module preferentially present in Planctomycetes, Verrucomicrobia, and Lentisphaerae species possessing additional intracellular membranes, and possibly associated with the complex PVC cell plan. These genes are excellent candidates for future functional studies.;Within the set of proteins associated with PVC intracellular membranes, we detected over-representation of proteins bearing signal peptides. These sequences target proteins for translocation via the Sec pathway to the cytoplasmic membrane, periplasm, outer membrane, or cell exterior in Gram-negative bacteria, or to the endoplasmic reticulum in eukaryotic cells. This led us to hypothesize that in membrane-bearing PVC bacteria, Sec pathway proteins and/or signal peptides have undergone functional shifts to allow protein targeting to new destinations inside the cell. Systematic examination of compartmentalization-associated gene families showed that they bear canonical signal peptides, which indicates that they should be recognized and targeted by the canonical Sec translocase. Within the Sec pathway components, we found domain rearrangements and gene duplications affecting the SecA ATPase in a number of PVC genomes. Further analysis of the SecA2-related system revealed a potentially novel secretion system related to both the Sec pathway and the type I secretion system.;In summary, the work described in this thesis has made contributions to multiple areas of PVC comparative genomic analysis, leading to an improvement in our understanding of the evolutionary structure and dynamics of the super-phylum, as well as identification of candidate genes underlying the cellular and molecular biology features of PVC organisms.