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Title: Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

Abstract

CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Furthermore, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity.

Authors:
; ORCiD logo; ORCiD logo; ; ; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1482289
Alternate Identifier(s):
OSTI ID: 1563978
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Science
Additional Journal Information:
Journal Name: Science Journal Volume: 362 Journal Issue: 6416; Journal ID: ISSN 0036-8075
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Harrington, Lucas B., Burstein, David, Chen, Janice S., Paez-Espino, David, Ma, Enbo, Witte, Isaac P., Cofsky, Joshua C., Kyrpides, Nikos C., Banfield, Jillian F., and Doudna, Jennifer A. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. United States: N. p., 2018. Web. doi:10.1126/science.aav4294.
Harrington, Lucas B., Burstein, David, Chen, Janice S., Paez-Espino, David, Ma, Enbo, Witte, Isaac P., Cofsky, Joshua C., Kyrpides, Nikos C., Banfield, Jillian F., & Doudna, Jennifer A. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. United States. doi:10.1126/science.aav4294.
Harrington, Lucas B., Burstein, David, Chen, Janice S., Paez-Espino, David, Ma, Enbo, Witte, Isaac P., Cofsky, Joshua C., Kyrpides, Nikos C., Banfield, Jillian F., and Doudna, Jennifer A. Thu . "Programmed DNA destruction by miniature CRISPR-Cas14 enzymes". United States. doi:10.1126/science.aav4294.
@article{osti_1482289,
title = {Programmed DNA destruction by miniature CRISPR-Cas14 enzymes},
author = {Harrington, Lucas B. and Burstein, David and Chen, Janice S. and Paez-Espino, David and Ma, Enbo and Witte, Isaac P. and Cofsky, Joshua C. and Kyrpides, Nikos C. and Banfield, Jillian F. and Doudna, Jennifer A.},
abstractNote = {CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Furthermore, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity.},
doi = {10.1126/science.aav4294},
journal = {Science},
number = 6416,
volume = 362,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1126/science.aav4294

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Cited by: 28 works
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Works referenced in this record:

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
journal, October 2015

  • Zetsche, Bernd; Gootenberg, Jonathan S.; Abudayyeh, Omar O.
  • Cell, Vol. 163, Issue 3, p. 759-771
  • DOI: 10.1016/j.cell.2015.09.038

An updated evolutionary classification of CRISPR–Cas systems
journal, September 2015

  • Makarova, Kira S.; Wolf, Yuri I.; Alkhnbashi, Omer S.
  • Nature Reviews Microbiology, Vol. 13, Issue 11, p. 722-736
  • DOI: 10.1038/nrmicro3569

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016

  • Letunic, Ivica; Bork, Peer
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw290

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014


IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
  • Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
  • DOI: 10.1093/nar/gkt919

Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes
journal, November 2015


Diversity and evolution of class 2 CRISPR–Cas systems
journal, January 2017

  • Shmakov, Sergey; Smargon, Aaron; Scott, David
  • Nature Reviews Microbiology, Vol. 15, Issue 3
  • DOI: 10.1038/nrmicro.2016.184

The chemistry of Cas9 and its CRISPR colleagues
journal, October 2017


Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity
journal, February 2015

  • Nuñez, James K.; Lee, Amy S. Y.; Engelman, Alan
  • Nature, Vol. 519, Issue 7542
  • DOI: 10.1038/nature14237

DNase H Activity of Neisseria meningitidis Cas9
journal, October 2015


CRISPRDetect: A flexible algorithm to define CRISPR arrays
journal, May 2016


Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015

  • Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
  • Nature, Vol. 523, Issue 7559
  • DOI: 10.1038/nature14486

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
journal, May 2007

  • Grissa, I.; Vergnaud, G.; Pourcel, C.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm360

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection
journal, September 2016

  • East-Seletsky, Alexandra; O’Connell, Mitchell R.; Knight, Spencer C.
  • Nature, Vol. 538, Issue 7624
  • DOI: 10.1038/nature19802

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity
journal, February 2018


A Broad-Spectrum Inhibitor of CRISPR-Cas9
journal, September 2017


CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA
journal, March 2018


Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

A thermostable Cas9 with increased lifetime in human plasma
journal, November 2017

  • Harrington, Lucas B.; Paez-Espino, David; Staahl, Brett T.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/s41467-017-01408-4

CRISPR-Cas: Adapting to change
journal, April 2017

  • Jackson, Simon A.; McKenzie, Rebecca E.; Fagerlund, Robert D.
  • Science, Vol. 356, Issue 6333
  • DOI: 10.1126/science.aal5056

Diversity, classification and evolution of CRISPR-Cas systems
journal, June 2017


Guide-bound structures of an RNA-targeting A-cleaving CRISPR–Cas13a enzyme
journal, September 2017

  • Knott, Gavin J.; East-Seletsky, Alexandra; Cofsky, Joshua C.
  • Nature Structural & Molecular Biology, Vol. 24, Issue 10
  • DOI: 10.1038/nsmb.3466

Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection
journal, January 2008


CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
journal, March 2007


IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1044

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
journal, February 2012

  • Yosef, Ido; Goren, Moran G.; Qimron, Udi
  • Nucleic Acids Research, Vol. 40, Issue 12
  • DOI: 10.1093/nar/gks216

The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a
journal, August 2017


Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan
journal, February 2018

  • Yoshida, Mitsuhiro; Mochizuki, Tomohiro; Urayama, Syun-Ichi
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.00075

HMMER web server: interactive sequence similarity searching
journal, May 2011

  • Finn, R. D.; Clements, J.; Eddy, S. R.
  • Nucleic Acids Research, Vol. 39, Issue suppl
  • DOI: 10.1093/nar/gkr367

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
journal, June 2016

  • Abudayyeh, Omar O.; Gootenberg, Jonathan S.; Konermann, Silvana
  • Science, Vol. 353, Issue 6299
  • DOI: 10.1126/science.aaf5573

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016

  • Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13219

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
journal, November 2015


Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016

  • Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw929

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999

  • Ogata, H.; Goto, S.; Sato, K.
  • Nucleic Acids Research, Vol. 27, Issue 1
  • DOI: 10.1093/nar/27.1.29

WebLogo: A Sequence Logo Generator
journal, May 2004

  • Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
  • Genome Research, Vol. 14, Issue 6, p. 1188-1190
  • DOI: 10.1101/gr.849004

New CRISPR–Cas systems from uncultivated microbes
journal, December 2016

  • Burstein, David; Harrington, Lucas B.; Strutt, Steven C.
  • Nature, Vol. 542, Issue 7640
  • DOI: 10.1038/nature21059

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
journal, March 2011

  • Deltcheva, Elitza; Chylinski, Krzysztof; Sharma, Cynthia M.
  • Nature, Vol. 471, Issue 7340
  • DOI: 10.1038/nature09886

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015

  • Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
  • Current Biology, Vol. 25, Issue 6
  • DOI: 10.1016/j.cub.2015.01.014