Mueller Linda, Bertelli Claire, Pillonel Trestan, Salamin Nicolas, Greub Gilbert
Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland.
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Genome Biol Evol. 2017 Jun 1;9(6):1432-1449. doi: 10.1093/gbe/evx074.
Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture.
在过去十年中，抗变形虫的微生物引起了极大的关注。其中，一些大型DNA病毒拥有长达2.5 Mb的巨大基因组，超过了小型细菌基因组的大小。这些基因组在突变、缺失和基因获取方面的基因组进化速率尚不清楚。鉴于病毒基因组具有高度可塑性，我们对巨型病毒目成员洛桑病毒346 kb的基因组微进化进行了研究。因此，洛桑病毒在棘阿米巴内共培养了一年多。尽管突变数量较少，但该病毒在12个月后基因组减少了3.7%。通过将洛桑病毒与专性细胞内细菌洛桑埃斯特雷拉菌在棘阿米巴中共培养一年，研究了其在同域条件下的基因组进化。每3个月对培养物进行一次传代。基因组测序显示，在这些条件下，洛桑病毒和洛桑埃斯特雷拉菌的基因组都很稳定，没有发生重大重排。事实上，一年后，洛桑病毒和洛桑埃斯特雷拉菌每次培养分别获得了2至7个和4至10个突变。有趣的是，在不同的传代培养物中观察到洛桑病毒内切酶编码基因存在不同的突变，突出了该基因产物在洛桑病毒复制中的重要性。相反，洛桑埃斯特雷拉菌的突变主要位于一个编码磷酸烯醇丙酮酸 - 蛋白质磷酸转移酶（PtsI）的基因中，该酶与糖代谢有关。此外，在我们的培养条件和分析中，我们在一年的共培养过程中未检测到水平基因转移。
