Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have resequenced the 9.2-Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10-Mb genome of G. massiliana Soil9, the 7.9-Mb genome of CJuql4, and the 6.7-Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multidomain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, leucine-rich repeat, tetratricopeptide repeat and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length, and protein domain composition patterns.

中文翻译：

---

具有复杂细胞结构的扁平菌细菌中的特异化和新的蛋白质结构。

扁平菌门细菌具有独特的细胞计划，并带有精细的细胞内膜系统，因此类似于真核细胞。这些显着特征的起源和演变一直存在争议。为了研究复杂的细胞结构细菌的进化基因组，我们已经重新排序的模式生物的9.2-MB基因组Gemmata obscuriglobus和测序的10-MB基因组G. massiliana Soil9，CJuql4的7.9 MB的基因组，以及6.7固定的Tuwongella的Mb基因组，全部属于芽孢杆菌科。对扁平菌进行的基因通量分析表明，新蛋白家族大量出现在拟南芥中。菊科。扩展的蛋白质家族具有独特的多结构域结构，该结构由原核生物的特征域组成，例如胞浆外sigma因子的sigma因子域，以及在真核生物中增殖的域，例如WD40，富含亮氨酸的重复序列，四三肽重复序列和Ser / Thr激酶结构域。与大多数其他细菌中的蛋白质相比，在芽孢科中具有可识别结构域的蛋白质具有更长的长度和连接子，并且分析表明这些特征祖先存在于扁平菌中。蛋白质长度分布曲线的广泛比较揭示了原核生物中最长的蛋白质与真核生物中最短的蛋白质之间存在重叠。我们得出的结论是，浮游生物中的蛋白质与真核生物之间的许多相似性是由于趋同进化而引起的，并且在原核生物和真核生物之间就基因的寄生性，蛋白质长度和蛋白质结构域组成特征等方面没有严格的界限。