Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

Well-studied innate immune systems exist throughout bacteria and archaea, but a more recently discovered genomic locus may offer prokaryotes surprising immunological adaptability. Mediated by a cassette-like genomic locus termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), the microbial adaptive immune system differs from its eukaryotic immune analogues by incorporating new immunities unidirectionally. CRISPR thus stores genomically recoverable timelines of virus-host coevolution in natural organisms refractory to laboratory cultivation. Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. This ‘trailer-end conservation’ occurs despite rapid viral mutation and despite rapid prokaryotic genomic deletion. The trailer-ends of many reconstructed CRISPR loci are also largely identical across a population. ‘Trailer-end clonality’ occurs despite predictions of host immunological diversity due to negative frequency dependent selection (kill the winner dynamics). Statistical clustering and model simulations explain this lack of diversity by capturing rapid selective sweeps by highly immune CRISPR lineages. Potentially explaining ‘trailer-end conservation,’ we record the first example of a viral bloom overwhelming a CRISPR system. The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. Our results thus link documented patterns of genomic conservation in CRISPR loci to an evolutionary advantage against persistent viruses. By maintaining old immunities, selection may be tuning CRISPR-mediated immunity against viruses reemerging from lysogeny or migration.

细菌与古菌中广泛存在研究较为透彻的先天免疫系统，但近年发现的一类基因组位点或许能为原核生物带来令人惊喜的免疫适应性。这种由一类被称为成簇的规律间隔的短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR）的盒状基因组位点介导的微生物适应性免疫系统，与真核生物的同类免疫系统不同，其以单向方式获取新的免疫能力。因此，CRISPR可在难以进行实验室培养的自然生物中，存储病毒与宿主共进化的、可从基因组中恢复的时间线记录。本研究将CRISPR-病毒共进化的种群遗传学数学模型与六年的宏基因组测序数据相结合，将CRISPR位点可恢复的基因组动态，与自然群落中尚不明确的病毒与宿主种群动态关联起来。对酸性矿山排水系统的宏基因组重构研究显示，CRISPR位点在数千个微生物世代中，能以碱基对级精度保留祖先免疫元件。尽管病毒发生快速突变、原核生物基因组存在快速缺失现象，这种"尾随端保守性"依然存在。在同一种群中，多数重构得到的CRISPR位点的尾随端也几乎完全一致。尽管根据负频率依赖选择（即"杀伤赢家"动态）的预测，宿主免疫系统应呈现多样性，但这种"尾随端克隆性"依然出现。统计聚类与模型模拟通过捕捉高免疫性CRISPR谱系的快速选择性清除，解释了这种多样性缺失的现象。本研究记录了首个病毒暴发性扩增压倒CRISPR系统的案例，这或许能解释"尾随端保守性"的成因。尽管这些多克隆病毒拥有此前被宿主CRISPR位点靶向的序列，它们仍实现了暴发性扩增。模拟实验显示，CRISPR位点中随机基因组缺失的增加会清除对长寿命病毒序列的免疫管控，使得多克隆病毒得以暴发性扩增，并降低宿主的适合度。因此，本研究的结果将CRISPR位点中已被记录的基因组保守模式，与对抗持续性病毒的进化优势关联了起来。通过保留旧有的免疫能力，自然选择或许会调整CRISPR介导的免疫系统，以对抗从溶原状态复苏或通过迁移重新出现的病毒。