Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity.
Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity.
复制标题
噬菌体基因表达和宿主反应导致CRISPR免疫的感染依赖性成本。
DOI：
10.1038/s41396-020-00794-w
复制
发表时间：
2021-03
期刊：
影响因子：
--
通讯作者：
Westra ER
中科院分区：
文献类型：
--
作者：
Meaden S;Capria L;Alseth E;Gandon S;Biswas A;Lenzi L;van Houte S;Westra ER
CRISPR-Cas免疫系统广泛存在于细菌和古细菌中，但并非无处不在。先前的研究表明，CRISPR免疫与感染诱导的适应性成本有关，这可能有助于解释观察到的斑块分布。然而，这一成本的机械基础仍然不清楚。以铜绿假单胞菌PA 14及其噬菌体DMS 3vir为模型，进行了噬菌体介导的30天进化实验。我们证明，尽管最初选择了CRISPR，但在随后的再感染后，携带噬菌体受体突变的细菌迅速侵入人群。然后，我们测试了CRISPR观察到的成本的三种潜在机制：（1）来自自靶向间隔区的获得的自身免疫，（2）来自cas基因表达增加的免疫病理学或能量成本，以及（3）在CRISPR介导的切割之前由噬菌体基因表达引起的毒性。我们发现，在免疫系统清除感染之前，病毒可以表达基因，这些基因的表达可能对宿主适应性产生负面影响。虽然感染不会导致cas基因的表达增加，但它确实会导致多种其他宿主过程的差异表达，这可能进一步导致CRISPR免疫的成本。相反，我们发现很少支持感染诱导的自身免疫和免疫病理学效应。因此，在CRISPR-Cas免疫系统切割基因组之前的噬菌体基因表达是对所观察到的噬菌体诱导的适应性成本的最简约的解释。
CRISPR-Cas immune systems are widespread in bacteria and archaea, but not ubiquitous. Previous work has demonstrated that CRISPR immunity is associated with an infection-induced fitness cost, which may help explain the patchy distribution observed. However, the mechanistic basis of this cost has remained unclear. Using Pseudomonas aeruginosa PA14 and its phage DMS3vir as a model, we perform a 30-day evolution experiment under phage mediated selection. We demonstrate that although CRISPR is initially selected for, bacteria carrying mutations in the phage receptor rapidly invade the population following subsequent reinfections. We then test three potential mechanisms for the observed cost of CRISPR: (1) autoimmunity from the acquisition of self-targeting spacers, (2) immunopathology or energetic costs from increased cas gene expression and (3) toxicity caused by phage gene expression prior to CRISPR-mediated cleavage. We find that phages can express genes before the immune system clears the infection and that expression of these genes can have a negative effect on host fitness. While infection does not lead to increased expression of cas genes, it does cause differential expression of multiple other host processes that may further contribute to the cost of CRISPR immunity. In contrast, we found little support for infection-induced autoimmunological and immunopathological effects. Phage gene expression prior to cleavage of the genome by the CRISPR-Cas immune system is therefore the most parsimonious explanation for the observed phage-induced fitness cost.