Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems.

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PubMed ID: 31130929

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Chen LX, Al-Shayeb B, Méheust R, Li WJ, Doudna JA, Banfield JF

Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00928

COMMENT: Using metagenomics sequencing the authors investigate CRISPR-Cas systems in Tibet hot springs, rich in genomes belonging to Candidate Phyla Radiation (CPR) taxa that have small genomes and rarely encode CRISPR-Cas systems for phage defense. They find interesting systems in Roizmanbacteria in which sometimes multiple different systems coexist in the same genome. They also detect an interesting case with self-targeting spacers and a fragmented CasY gene.


Here, we conducted a genome-resolved metagenomic investigation of hot spring microbiomes and recovered CRISPR systems mostly from Roizmanbacteria that involve CasY proteins that are divergent from published sequences

In the current study, we investigated the microbiomes of a series of hot springs in Tibet. CPR bacteria are relatively abundant in these thermal environments, and some of their genomes encode interesting and unusual CRISPR-Cas systems. Although uncommon overall, CRISPR-Cas systems are surprisingly frequently encoded in the genomes of members of the Roizmanbacteria, and multiple different systems coexist in some genomes. We identified many new examples of systems based on CasY and uncovered an intriguing example of a locus with self-targeting spacers and a fragmented CasY gene.


CRISPR-Cas systems are unexpectedly common in a subset of CPR bacteria, and the number, variety and potential functional diversity of these systems is greater than expected. It is already established that CRISPR-CasY systems from these intriguing and enigmatic bacteria will have biotechnological value.

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Raquel Tobes