CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged as an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and higher GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage is the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbour a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity. We propose that CRISPR-Cas acts as an important constraint to horizontal gene transfer, and the evolutionary mechanisms that ensure its maintenance or drive its loss are key to the ability of this pathogen to adapt to new niches and stressors.

CRISPR-Cas系统为细菌和古细菌提供了针对外源DNA的适应性免疫系统。然而，CRISPR-Cas 提供的免疫的异种性质提出了这些系统可能限制水平基因转移的可能性。在这里，我们在机会性病原体铜绿假单胞菌中测试了这一假设，该病原体已成为理解 CRISPR-Cas 功能的重要模型系统。在铜绿假单胞菌的多样性中，活跃的 CRISPR-Cas 系统与较小的基因组和较高的 GC 含量相关，这表明 CRISPR-Cas 抑制外源 DNA 的获取。尽管噬菌体是 CRISPR-Cas 间隔区的主要目标，但超过 80% 具有活性 CRISPR-Cas 系统的分离株都具有靶向整合接合元件 (ICE) 或质粒和 ICE 使用的保守接合转移机制的间隔区。与这些结果一致，含有活性 CRISPR-Cas 系统的基因组中原噬菌体和 ICE 的丰度较低。至关重要的是，具有活性 CRISPR-Cas 系统的基因组中的间隔区映射到 ICE 和噬菌体，这些ICE 和噬菌体被整合到缺乏 CRISPR-Cas 免疫性的密切相关基因组的染色体中。我们认为 CRISPR-Cas 是水平基因转移的重要限制因素，确保其维持或驱动其丢失的进化机制是该病原体适应新生态位和应激源的能力的关键。