Genomic evolution in bacteria from PVC super-phylum (Planctomycetes-Verrucomicrobiae-Chlamydiae)

La compréhension de l'évolution des génomes est un des enjeux clé de la biologie actuelle. Nous avons rédigé une revue littéraire consacrée à la contribution de la génomique dans la compréhension de la diversité, de l'évolution et des phénotypes d'un super-phylum bactérien, le super-phylum PVC (Planctomycetes, Verrucomicrobiae et Chlamydiae). Ces bactéries proviennent d'environnements variés et présentent des caractéristiques phénotypiques intéressantes. Les analyses génomiques ont révélé la grande diversité de ces espèces, mais ont aussi permis de reconstruire l'évolution de leurs génomes et d'expliquer l'apparition de certains phénotypes particuliers. Une partie de notre travail était consacré à l'étude de l'évolution et de l'impact de la présence d'un plan cellulaire particulier chez les bactéries PVC. Ce plan cellulaire est sujet a différentes interprétations et induirait la compartimentation des cellules en deux régions distinctes. Les résultats obtenus semblent indiquer que cette caractéristique n'induit pas une protection des génomes bactériens vis à vis des transferts de gènes horizontaux, comme on pourrait le supposer. En revanche les observations microscopiques réalisées sur deux espèces ont permis de mieux appréhender l'évolution de ce plan cellulaire. Nous avons, de plus, détecté une contribution de l'environnement concernant la sélection des gènes transférés. Il semblerait que les gènes transférés soient en effet sélectionnés selon leurs fonctions par les différents environnements.Nos travaux ont donc permis d'améliorer la compréhension des relations entre l'évolution, les phénotypes et l'environnement, en particulier chez les bactéries du super-phylum PVC.The comprehension of genomes evolution is a key issue of modern biology.We wrote a review dedicated to the genomic contribution in comprehension of diversity, evolution and phenotypes, in a bacterial super-phylum named PVC (for Planctomycetes, Verrucomicrobiae and Chlamydiae). These bacteria are distributed in varied environments and present specific phenotypic characteristics. Genomic analyzes revealed the important diversity of these species and allow also to reconstruct the genomes evolution and, in some cases, to explain the presence of specific phenotypes. One part of our work was dedicated to the study of evolution and impact of one of this phenotype, the special cell plan detected in PVC bacteria. This original cell plan is subject to different interpretations and induces the compartmentalization of cells in two different regions, whom one containing the nucleoid. Our results indicate that this feature has probably no role in the protection of bacterial genomes against horizontal genes transfers, so, its function is still unknown. Microscopic observations of two species from PVC super-phylum permit to better understand the evolution of the special cell plan. The environment seems to contribute in the genomes evolution, by selection of genes transferred. Genes transferred are probably selected according to their functions by the different environments.Our works allowed to improve the knowledge about relations between evolution, genomes, phenotypes and environment, especially in bacteria from PVC super-phylum

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum

International audienceBackground: Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan. Results: Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats. Conclusions: The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions

Compartmentalization in PVC super-phylum: evolution and impact

International audienceBackground: The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomyces and several Verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). The evolution and function of this cell plan is still subject to debate. In this work, we hypothesized that it could play a role in protection of the bacterial DNA, especially against Horizontal Genes Transfers (HGT). Therefore, 64 bacterial genomes belonging to seven different phyla (whose four PVC phyla) were studied. We reconstructed the evolution of the cell plan as precisely as possible, thanks to information obtained by bibliographic study and electronic microscopy. We used a strategy based on comparative phylogenomic in order to determine the part occupied by the horizontal transfers for each studied genomes. Results: Our results show that the bacteria Simkania negevensis (Chlamydiae) and Coraliomargarita akajimensis (Verrucomicrobiae), whose cell plan were unknown before, are compartmentalized, as we can see on the micrographies. This is one of the first indication of the presence of an intracytoplasmic membrane in a Chlamydiae. The proportion of HGT does not seems to be related to the cell plan of bacteria, suggesting that compartmentalization does not induce a protection of bacterial DNA against HGT. Conversely, lifestyle of bacteria seems to impact the ability of bacteria to exchange genes. Conclusions: Our study allows a best reconstruction of the evolution of intracytoplasmic membrane, but this structure seems to have no impact on HGT occurrences

Kebijakan Anti Dumping Dan Trade Deflection: Studi Kasus Synthetic Staple Fibre Polyester (PSF)

. This research empirically examines whether a country\u27s anti dumping policy can distort export of another country to third markets. This research tries to explore about trade deflection of Indonesia\u27s export on Synthetic Staple Fibre Polyester (PSF) HS 550320 to non-European Union as the result of European Union\u27s (EU) anti dumping policy on Indonesia. This research uses panel data model (fixed effects) and 20 countries (non-European Union) of Indonesia\u27s PSF export during ten years (1996-2005). We find evidence that trade deflection for Indonesia\u27s export on Synthetic Staple Fibre Polyester (PSF) HS 550320 occurred. Because of European Union had imposed anti dumping duty on Indonesia, Indonesia\u27s export to nonEuropean Union had increased ranged from 25 percent to 44 percent. This result shows that dumping duty from European Union does not fully carry out negative effect for Indonesia, furthermore thisphenomena can be used as ”early warning” for Indonesia both for case of Indonesia as exporting country or third countries

Additional file 2: of Compartmentalization in PVC super-phylum: evolution and impact

Characteristics of studied species. This table presents the lifestyles, genomes and proteomes features of each species studied. (PDF 125 kb

Study of genome evolution among traditional bakery yeasts in relation to domestication

Study of genome evolution among traditional bakery yeasts in relation to domestication. NGS 201