CRISPR介导的病毒-细菌协同进化的非经典相图
Nonclassical phase diagram for virus bacterial co-evolution mediated by CRISPR
摘要：
CRISPR是新发现的原核免疫系统。具有这种系统的细菌和古生菌将来自入侵病毒的遗传物质整合到它们的基因组中，从而提供对类似病毒未来感染的保护。原核细胞与病毒共存的条件是进化生物学中一个有趣的问题。在这项工作中，我们展示了一个有趣的相图的病毒灭绝概率，这是更复杂的比经典的捕食者-食饵模型。由于CRISPR包含遗传物质，病毒面临着进化的压力，以逃避CRISPR的识别。当细菌具有较小的间隔区删除率时，细菌和病毒可以共存的新参数区域出现，并且导致细菌和病毒的共存模式更加复杂。例如，当病毒突变率较低时，病毒灭绝概率随细菌暴露率非单调变化。病毒和细菌的协同进化不仅改变了病毒的灭绝概率，而且改变了细菌的种群结构。此外，我们表明，当病毒具有多个原型间隔区时，重组是病毒逃避CRISPR识别的成功策略，为实验提出的重组介导的逃逸机制提供了支持。最后，我们建议，可重入相图中，其中，在低间隔区缺失率作为暴露率的函数，细菌可以通过三个阶段的灭绝和两个阶段的丰度进展，是一个实验测试的现象。
英文摘要：
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The conditions for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape the recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria co-evolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the reentrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon.
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