洛克菲勒大学的Luciano A. Marraffini研究团队近日合作取得一项新的研究成果，他们发现Cas13诱导的细菌休眠能够阻止CRISPR抗性噬菌体的爆发。该项研究成果发表在2019年6月13日出版的《自然》杂志上。

原核生物的CRISPR基因座是由质粒和噬菌体来源的短片段（又被称为间隔序列）所分隔开的30到40bp间隔重复序列。这些基因座能够转录产生短的CRISPR RNA，来指导CRISPR相关核酸酶Cas去识别并降解外来的互补序列。因此，CRISPR与Cas9构成了细菌的免疫系统。与大多数能够摧毁外来DNA的Cas核酸酶不同，第六类的效应核酸酶Cas13用RNA来指引发现互补的RNA转录本，并能够清除序列特异的顺式RNA与非特异的反式RNA。尽管前人猜测Cas13能够抵抗RNA噬菌体，但第六类的间隔序列却被发现与双链DNA噬菌体的序列互补，由此提示Cas13为抵御后者提供免疫防御。然而，Cas13能否用其顺式和反式RNA清除活力来抵御双链DNA噬菌体，以及如何实现这一功能尚不清楚。

在这项工作中，研究人员发现对Cas13介导的转录本反式清除不仅切割了噬菌体的RNA也切割了宿主自身的RNA，从而引起宿主细胞的生长停滞，并终止噬菌体的感染周期。这一行为能够减少噬菌体的数量，并为未受感染的细菌提供群体免疫。由于Cas13切割的非特异性，那些靶序列有突变的噬菌体按理应该是能够逃避CRISPR系统的，但仍然能够被野生型噬菌体激活的Cas13所清除。因此，第六类CRISPR系统是通过其在宿主发挥功能而不是直接靶向噬菌体，那么这不仅为细菌提供了强有力的防御来抵抗DNA噬菌体也能够阻止对CRISPR已产生抗性的噬菌体。

附：英文原文

Title: Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage

Author: Alexander J. Meeske, Sandra Nakandakari-Higa, Luciano A. Marraffini

Issue&Volume: Volume 570 Issue 7760, 13 June 2019

Abstract: Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci in prokaryotes are composed of 30–40-base-pair repeats separated by equally short sequences of plasmid and bacteriophage origin known as spacers1,2,3. These loci are transcribed and processed into short CRISPR RNAs (crRNAs) that are used as guides by CRISPR-associated (Cas) nucleases to recognize and destroy complementary sequences (known as protospacers) in foreign nucleic acids4,5. In contrast to most Cas nucleases, which destroy invader DNA4,5,6,7, the type VI effector nuclease Cas13 uses RNA guides to locate complementary transcripts and catalyse both sequence-specific cis- and non-specific trans-RNA cleavage8. Although it has been hypothesized that Cas13 naturally defends against RNA phages8, type VI spacer sequences have exclusively been found to match the genomes of double-stranded DNA phages9,10, suggesting that Cas13 can provide immunity against these invaders. However, whether and how Cas13 uses its cis- and/or trans-RNA cleavage activities to defend against double-stranded DNA phages is not understood. Here we show that trans-cleavage of transcripts halts the growth of the host cell and is sufficient to abort the infectious cycle. This depletes the phage population and provides herd immunity to uninfected bacteria. Phages that harbour target mutations, which easily evade DNA-targeting CRISPR systems11,12,13, are also neutralized when Cas13 is activated by wild-type phages. Thus, by acting on the host rather than directly targeting the virus, type VI CRISPR systems not only provide robust defence against DNA phages but also prevent outbreaks of CRISPR-resistant phage.

DOI: https://doi.org/10.1038/s41586-019-1257-5

Source: https://www.nature.com/articles/s41586-019-1257-5