Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Centre National de la Recherche Scientifique Unité Mixte de Recherche (UMR) 7278, Institut de Recherche pour le Développement (IRD) 3R198, INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Aix-Marseille University Marseille, France.
Front Cell Infect Microbiol. 2012 Jul 5;2:91. doi: 10.3389/fcimb.2012.00091. eCollection 2012.
Acanthamoeba polyphaga Mimivirus has been subcultured 150 times on germ-free amoebae. This allopatric niche is very different from that found in the natural environment, where the virus is in competition with many other organisms. In this experiment, substantial gene variability and loss occurred concurrently with the emergence of phenotypically different viruses. We sought to quantify the respective roles of Lamarckian and Darwinian evolution during this experiment. We postulated that the Mimivirus genes that were down-regulated at the beginning of the allopatric laboratory culture and inactivated after 150 passages experienced Lamarckian evolution because phenotypic modifications preceded genotypic modifications, whereas we considered that genes that were highly transcribed in the new niche but were later inactivated obeyed Darwinian rules. We used the total transcript abundances and sequences described for the genes of Mimivirus at the beginning of its laboratory life and after 150 passages in allopatric culture on Acanthamoeba spp. We found a statistically significant positive correlation between the level of gene expression at the beginning of the culture and gene inactivation during the 150 passages. In particular, the mean transcript abundance at baseline was significantly lower for inactivated genes than for unchanged genes (165 ± 589 vs. 470 ± 1,625; p < 1e-3), and the mean transcript levels during the replication cycle of Mimivirus M1 were up to 8.5-fold lower for inactivated genes than for unchanged genes. In addition, proteins tended to be less frequently identified from purified virions in their early life in allopatric laboratory culture if they were encoded by variable genes than if they were encoded by conserved genes (9 vs. 15%; p = 0.062). Finally, Lamarckian evolution represented the evolutionary process encountered by 63% of the inactivated genes. Such observations may be explained by the lower level of DNA repair of useless genes.
多噬棘阿米巴虫曼氏拟病毒已在无菌阿米巴中连续传代培养了 150 次。这种异地小生境与病毒在自然环境中所处的小生境大不相同，在自然环境中，病毒与许多其他生物竞争。在这项实验中，大量的基因变异和丢失同时伴随着表型不同的病毒的出现。我们试图量化拉马克进化和达尔文进化在这个实验中的各自作用。我们假设，在异地实验室培养的早期被下调且在 150 次传代后失活的曼氏拟病毒基因经历了拉马克进化，因为表型修饰先于基因型修饰，而我们认为，在新小生境中高度转录但后来失活的基因则遵循达尔文法则。我们使用了曼氏拟病毒在实验室生活开始时以及在异地培养的 150 次传代后在棘阿米巴属上的所有基因的总转录丰度和序列。我们发现，在培养开始时的基因表达水平与 150 次传代过程中的基因失活之间存在显著的正相关。特别是，失活基因的基线平均转录丰度显著低于未改变基因（165 ± 589 与 470 ± 1,625；p < 1e-3），并且在曼氏拟病毒 M1 的复制周期中，失活基因的平均转录水平比未改变基因低 8.5 倍。此外，如果编码可变基因的基因比编码保守基因的基因在其早期的异地实验室培养中更频繁地从纯化的病毒粒子中被鉴定出来（9 与 15%；p = 0.062）。最后，拉马克进化代表了 63%失活基因所经历的进化过程。这些观察结果可能是由于无用基因的 DNA 修复水平较低所致。
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