New CRISPR–Cas systems from uncultivated microbes

Abstract

Using a metagenomic approach, three types of CRISPR–Cas systems have been discovered in uncultivated bacterial and archaeal hosts from a variety of different environments. Current CRISPR–Cas technology is based on systems identified from cultured bacteria, whereas the enzymes from the numerous prokaryotes that have not been cultured have remained unexplored. By using cultivation-independent genome-resolved metagenomics, Jillian Banfield, Jennifer Doudna and colleagues identify and then functionally characterize new CRISPR–Cas systems. These include the first reported Cas9 in the archaeal domain of life, which was thought to lack such systems, as well as compact CRISPR–CasX and CRISPR–CasY systems. Genomic exploration of environmental microbial communities gives access to unprecedented genome diversity with the potential to revolutionize microbe-based biotechnologies. CRISPR–Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA1,2. Class 2 CRISPR–Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences3,4. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research5. However, current CRISPR–Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms6,7. Here, using genome-resolved metagenomics, we identify a number of CRISPR–Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR–Cas system. In bacteria, we discovered two previously unknown systems, CRISPR–CasX and CRISPR–CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

Cite this article

Burstein, D., Harrington, L., Strutt, S. et al. New CRISPR–Cas systems from uncultivated microbes. Nature 542, 237–241 (2017). https://doi.org/10.1038/nature21059

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