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The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

Journal Article · · Science
 [1];  [1];  [1];  [1];  [1];  [2];  [3];  [4];  [5];  [1];  [5];  [1]
  1. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  2. Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA.; Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.; Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
  3. Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.
  4. Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA.; Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
  5. National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
Tracing the origin of CRISPR-Cas

CRISPR-Cas systems have transformed genome editing and other biotechnologies; however, the broader origins and diversity of RNA-guided nucleases have largely remained unexplored. Altae-Tranet al. show that three distinct transposon-encoded proteins, IscB, IsrB, and TnpB, are naturally occurring, reprogrammable RNA-guided DNA nucleases (see the Perspective by Rousset and Sorek). In addition to identifying diverse guide-encoding mechanisms, the authors elucidate the evolutionary relationship between IsrB, IscB, and CRISPR-Cas9. Overall, these newly characterized systems, called OMEGA (for obligate mobile element–guided activity) systems, are found in all domains of life and may be harnessed for biotechnology development. —DJ

Research Organization:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC02-05CH11231
OSTI ID:
1982955
Journal Information:
Science, Journal Name: Science Journal Issue: 6563 Vol. 374; ISSN 0036-8075
Publisher:
AAAS
Country of Publication:
United States
Language:
English

References (61)

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity journal June 2012
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era journal February 2020
ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs journal December 2015
R2R - software to speed the depiction of aesthetic consensus RNA secondary structures journal January 2011
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria journal September 2012
A catalogue of biochemically diverse CRISPR-Cas9 orthologs journal November 2020
Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions journal August 2017
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability journal January 2013
The principles of guiding by RNA: chimeric RNA–protein enzymes journal April 2006
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets journal October 2017
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification journal January 2014
Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea journal March 2015
Silhouettes: A graphical aid to the interpretation and validation of cluster analysis journal November 1987
Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis journal May 2018
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA journal February 2014
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation journal February 2014
The Biology of CRISPR-Cas: Backward and Forward journal March 2018
Improved microbial gene identification with GLIMMER journal December 1999
A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs journal November 2016
The Prevalence and Impact of Model Violations in Phylogenetic Analysis journal September 2019
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal December 2009
TIGRFAMs: a protein family resource for the functional identification of proteins journal January 2001
BLAST+: architecture and applications journal January 2009
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System journal October 2015
Bacterial insertion sequences: their genomic impact and diversity journal September 2014
Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq journal June 2020
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference journal January 2004
Cutadapt removes adapter sequences from high-throughput sequencing reads journal May 2011
Infernal 1.1: 100-fold faster RNA homology searches journal September 2013
HH-suite3 for fast remote homology detection and deep protein annotation journal September 2019
Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants journal December 2019
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies journal January 2014
Density-Based Clustering Based on Hierarchical Density Estimates book January 2013
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing journal May 2012
Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements journal January 2013
ViennaRNA Package 2.0 journal November 2011
CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems journal April 2018
Fast gapped-read alignment with Bowtie 2 journal March 2012
Compact graphical representation of phylogenetic data and metadata with GraPhlAn journal January 2015
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
Rfam 14: expanded coverage of metagenomic, viral and microRNA families journal November 2020
Pfam: The protein families database in 2021 journal October 2020
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010
Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae journal April 2017
Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration journal June 2019
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments journal January 2010
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity journal May 2014
ModelFinder: fast model selection for accurate phylogenetic estimates journal May 2017
Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. journal March 1996
Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence journal February 2017
UFBoot2: Improving the Ultrafast Bootstrap Approximation journal October 2017
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats journal June 2007
Diversity and evolution of class 2 CRISPR–Cas systems journal January 2017
CRISPResso2 provides accurate and rapid genome editing sequence analysis journal February 2019
Development of CRISPR-Cas systems for genome editing and beyond journal January 2019
A short history of guide RNAs journal December 2020
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III journal March 2011
Accelerated Profile HMM Searches journal October 2011
RNA-guided DNA insertion with CRISPR-associated transposases journal June 2019
A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins journal April 2014

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