Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
Cell Host Microbe. 2019 Sep 11;26(3):325-335.e5. doi: 10.1016/j.chom.2019.08.008. Epub 2019 Sep 3.
Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.
噬菌体在人类胃肠道中大量存在，但它们与肠道细菌的相互作用仍知之甚少，特别是在 CRISPR-Cas 免疫方面。在这里，我们表明，在流行的肠道放线菌 Eggerthella lenta 中的 I-C 型 CRISPR-Cas 系统被转录，并足以特异性靶向外来和染色体 DNA。对来自 (meta)基因组的 E. lenta CRISPR-Cas 系统的比较分析根据 cas 序列相似性和间隔子内容揭示了 2 个不同的分支。我们组装了一个人类病毒组数据库 (HuVirDB)，包含 1831 个富含病毒 DNA 的样本，以识别原间隔子。这揭示了大多数间隔子的匹配，与其他数据库相比有显著增加，并发现了“超靶向”噬菌体序列，其中包含多个被多个 E. lenta 菌株靶向的原间隔子。最后，我们确定了观察到的间隔子-原间隔子对的位置错配容忍度。这项工作强调了合并计算和实验方法来确定 CRISPR-Cas 系统的功能和靶标的效用。
