Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

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.

doi:10.1126/science.aav4294

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:

Harrington, Lucas B.;

;

; Paez-Espino, David; Ma, Enbo;

;

Publication Date:: Thu Oct 18 00:00:00 EDT 2018

Research Org.:: Lawrence Berkeley National Laboratory (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.

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                    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.  https://doi.org/10.1126/science.aav4294

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                    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.  https://doi.org/10.1126/science.aav4294.

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@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         = {Thu Oct 18 00:00:00 EDT 2018},

  month        = {Thu Oct 18 00:00:00 EDT 2018}

}

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Title: Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

Abstract

Citation Formats

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

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

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

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

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

Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression journal, January 2008

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

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

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

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

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

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

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

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

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2 concentrations : Genomic resolution of a high-CO journal, July 2016

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

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

Short motif sequences determine the targets of the prokaryotic CRISPR defence system journal, March 2009

CRISPR-Cas: Adapting to change journal, April 2017

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

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

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

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

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

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

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

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

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

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

WebLogo: A Sequence Logo Generator journal, May 2004

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

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

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

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

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

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

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

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

Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression
journal, January 2008

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

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

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

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

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

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

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

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

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO ₂ concentrations : Genomic resolution of a high-CO
journal, July 2016

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

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

Short motif sequences determine the targets of the prokaryotic CRISPR defence system
journal, March 2009

CRISPR-Cas: Adapting to change
journal, April 2017

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

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

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

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

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

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

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

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

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

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

WebLogo: A Sequence Logo Generator
journal, May 2004

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

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

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