New CRISPR–Cas systems from uncultivated microbes

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

doi:10.1038/nature21059

Title: New CRISPR–Cas systems from uncultivated microbes

Journal Article · 21 December 2016 · Nature (London)

DOI: https://doi.org/10.1038/nature21059 · OSTI ID:1379729

Burstein, David ^[1]; Harrington, Lucas B. ^[2]; Strutt, Steven C. ^[2]; Probst, Alexander J. ^[1]; Anantharaman, Karthik ^[1]; Thomas, Brian C. ^[1]; Doudna, Jennifer A. ^[3]; Banfield, Jillian F. ^[4]

Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Sciences
Univ. of California, Berkeley, CA (United States). Department of Molecular and Cell Biology
Univ. of California, Berkeley, CA (United States). Department of Molecular and Cell Biology, Howard Hughes Medical Institute, Innovative Genomics Initiative, and MBIB Division
Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Sciences and Department of Environmental Science, Policy, and Management

We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. 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 organisms. 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. Lastly, 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379729

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7640 Vol. 542; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering Lone, Bilal Ahmad; Karna, Shibendra Kumar Lal; Ahmad, Faiz Genetics Research International, Vol. 2018 https://doi.org/10.1155/2018/3797214	journal	September 2018
Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts Bor, B.; Collins, A. J.; Murugkar, P. P. Journal of Dental Research, Vol. 99, Issue 6 https://doi.org/10.1177/0022034520905792	journal	February 2020
Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks Luo, Jiesi; Chen, Wei; Xue, Li BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-2939-6	journal	June 2019
HH-suite3 for fast remote homology detection and deep protein annotation Steinegger, Martin; Meier, Markus; Mirdita, Milot BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3019-7	journal	September 2019
Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants Wei, Shuai; Chen, He; Dzakah, Emmanuel Enoch Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-018-1619-6	journal	January 2019
On the global CRISPR array behavior in class I systems Toms, Alice; Barrangou, Rodolphe Biology Direct, Vol. 12, Issue 1 https://doi.org/10.1186/s13062-017-0193-2	journal	August 2017
CRISPR-like sequences in Helicobacter pylori and application in genotyping Bangpanwimon, Khotchawan; Sottisuporn, Jaksin; Mittraparp-arthorn, Pimonsri Gut Pathogens, Vol. 9, Issue 1 https://doi.org/10.1186/s13099-017-0215-8	journal	November 2017
Gene editing in dermatology: Harnessing CRISPR for the treatment of cutaneous disease Baker, Catherine; Hayden, Matthew S. F1000Research, Vol. 9 https://doi.org/10.12688/f1000research.23185.1	journal	January 2020
Gene editing in dermatology: Harnessing CRISPR for the treatment of cutaneous disease Baker, Catherine; Hayden, Matthew S. F1000Research, Vol. 9 https://doi.org/10.12688/f1000research.23185.2	journal	January 2020
Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae Wyres, Kelly L.; Wick, Ryan R.; Judd, Louise M. PLOS Genetics, Vol. 15, Issue 4 https://doi.org/10.1371/journal.pgen.1008114	journal	April 2019
CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci Rossi, Ciro C.; Souza-Silva, Thaysa; Araújo-Alves, Amanda V. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01545	journal	August 2017
Schizosaccharomyces pombe Can Reduce Acetic Acid Produced by Baijiu Spontaneous Fermentation Microbiota Song, Zhewei; Du, Hai; Zhang, Menghui Microorganisms, Vol. 7, Issue 12 https://doi.org/10.3390/microorganisms7120606	journal	November 2019
Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing Swarts, Daan C.; Jinek, Martin Wiley-Blackwell Publishing, Inc. https://doi.org/10.5167/uzh-168880	text	January 2018
Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms Krause, S.; Bremges, A.; Münch, P. C. Karlsruhe https://doi.org/10.5445/ir/1000071504	text	January 2017
The CRISPR/Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists Wolter, Felix; Puchta, Holger Karlsruhe https://doi.org/10.5445/ir/1000090977	text	January 2018
Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas Hickman, Alison B.; Kailasan, Shweta; Genzor, Pavol eLife, Vol. 9 https://doi.org/10.7554/elife.50004	journal	January 2020

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