Data from: Costs of CRISPR-Cas mediated resistance in Streptococcus thermophilus

CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.

CRISPR-Cas系统（CRISPR-Cas）是微生物中一类适应性序列特异性免疫机制。该系统为探究细菌与其病毒性病原体——噬菌体（bacteriophage）之间的协同进化提供了独特机遇。要全面阐明CRISPR-Cas系统的协同进化动力学，需明确抗感染免疫的代价幅度。本研究以携带至少两套功能性II型CRISPR-Cas系统的成熟经典模型系统——革兰氏阳性菌嗜热链球菌（Streptococcus thermophilus）及其烈性噬菌体2972为研究材料，通过单独培养生长测定与两两竞争实验，获取了多维度适合度指标。我们分别测定了该适应性免疫系统不同组分对应的适合度代价：Cas蛋白表达代价、通过额外获取间隔序列增强免疫记忆的组成型代价，以及噬菌体暴露时免疫激活的条件性代价。研究结果显示，Cas蛋白表达的代价尤为显著：Cas缺陷突变株的竞争能力高于携带功能性Cas蛋白的野生型菌株。通过获取最多4个噬菌体来源间隔序列以强化免疫记忆，并未伴随显著适合度代价。此外，噬菌体暴露条件下CRISPR-Cas系统的激活会引发显著但程度较轻的适合度代价。综上，本研究结果表明，CRISPR-Cas系统的代价主要源于防御系统的维持成本。最后我们探讨了该结果对CRISPR-Cas介导的免疫进化的启示意义。