Peach Luke J, Zhang Haoyun, Weaver Brian P, Boedicker James Q
Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States.
Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States.
Front Microbiol. 2025 Jan 20;15:1498959. doi: 10.3389/fmicb.2024.1498959. eCollection 2024.
CRISPR/Cas is an adaptive defense mechanism protecting prokaryotes from viruses and other potentially harmful genetic elements. Through an adaptation process, short "spacer" sequences, captured from these elements and incorporated into a CRISPR array, provide target specificity for the immune response. CRISPR arrays and array expansion are also central to many emerging biotechnologies. The rates at which spacers integrate into native arrays within bacterial populations have not been quantified. Here, we measure naïve spacer acquisition rates in Type I-E CRISPR, identify factors that affect these rates, and model this process fundamental to CRISPR/Cas defense. Prolonged Cas1-Cas2 expression produced fewer new spacers per cell on average than predicted by the model. Subsequent experiments revealed that this was due to a mean fitness reduction linked to array-expanded populations. In addition, the expression of heterologous non-homologous end-joining DNA-repair genes was found to augment spacer acquisition rates, translating to enhanced phage infection defense. Together, these results demonstrate the impact of intracellular factors that modulate spacer acquisition and identify an intrinsic fitness effect associated with array-expanded populations.
CRISPR/Cas是一种适应性防御机制，可保护原核生物免受病毒和其他潜在有害遗传元件的侵害。通过一个适应过程，从这些元件中捕获并整合到CRISPR阵列中的短“间隔区”序列为免疫反应提供了靶标特异性。CRISPR阵列和阵列扩展也是许多新兴生物技术的核心。间隔区整合到细菌群体内天然阵列中的速率尚未得到量化。在这里，我们测量了I-E型CRISPR中原始间隔区的获得率，确定了影响这些速率的因素，并对CRISPR/Cas防御的这一基本过程进行了建模。与模型预测相比，延长Cas1-Cas2的表达平均每个细胞产生的新间隔区更少。随后的实验表明，这是由于与阵列扩展群体相关的平均适应性降低所致。此外，发现异源非同源末端连接DNA修复基因的表达可提高间隔区的获得率，从而增强对噬菌体感染的防御。总之，这些结果证明了调节间隔区获得的细胞内因素的影响，并确定了与阵列扩展群体相关的内在适应性效应。
