Pinos Sandrine, Pontarotti Pierre, Raoult Didier, Merhej Vicky
Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331, France.
Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005, France.
BMC Evol Biol. 2017 Mar 9;17(1):75. doi: 10.1186/s12862-017-0921-3.
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.
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.
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.
水平转移在细菌基因组进化中起着重要作用，但它受到多种限制，包括与其他生物体相遇的生态机会、转移系统的存在以及转移基因的适应性。浮霉菌门、疣微菌门、衣原体（PVC）超门的细菌具有由胞内膜界定的区室化细胞结构，这可能构成另一种限制，对细菌进化有特别影响。在本研究中，我们研究了33个PVC物种基因组的进化，并关注水平转移序列的速率和性质与其栖息地和细胞结构的关系。
使用比较系统发育基因组学方法，我们表明栖息地影响细菌基因组内容的进化以及DNA水平转移（HT）的通量。因此，与生活在水中的细菌、脊椎动物体内的胞外细菌、变形虫体内的细菌以及脊椎动物体内的胞内细菌相比，土壤细菌、昆虫细菌和无处不在的细菌呈现出最高的水平转移平均值（每个物种平均分别为379次和110次转移事件，HT导致的每个基因组比例分别为7.6%和4.8%）。这些转移的伙伴主要是细菌生物体（94.9%）；它们使我们能够区分与变形菌交换更多的环境细菌和与厚壁菌交换更多的脊椎动物细菌。对水平转移的功能分析揭示了趋同进化，在不同栖息地的区室化细菌中，编码膜生物合成和脂质代谢的基因过度表达。
PVC物种中胞内膜的存在似乎根据其编码功能通过对转移DNA的选择来影响基因组的进化。
