Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Abstract
Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that the Methanosarcina mazei casposase can integrate varied forms of the casposon end in vitro, and recapitulates several properties of CRISPR-Cas integrases including site-specificity. The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization; this in turn led to preferred integration of single spacers over two transposon ends.
- Authors:
-
- National Institutes of Health (NIH), Bethesda, MD (United States). Lab. of Molecular Biology. National Inst. of Diabetes and Digestive and Kidney Diseases
- National Institutes of Health (NIH), Bethesda, MD (United States). Lab. of Cell and Molecular Biology. National Inst. of Diabetes and Digestive and Kidney Diseases
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1833697
- Resource Type:
- Accepted Manuscript
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Volume: 9; Journal ID: ISSN 2050-084X
- Publisher:
- eLife Sciences Publications, Ltd.
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Hickman, Alison B., Kailasan, Shweta, Genzor, Pavol, Haase, Astrid D., and Dyda, Fred. Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas. United States: N. p., 2020.
Web. doi:10.7554/elife.50004.
Hickman, Alison B., Kailasan, Shweta, Genzor, Pavol, Haase, Astrid D., & Dyda, Fred. Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas. United States. https://doi.org/10.7554/elife.50004
Hickman, Alison B., Kailasan, Shweta, Genzor, Pavol, Haase, Astrid D., and Dyda, Fred. Wed .
"Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas". United States. https://doi.org/10.7554/elife.50004. https://www.osti.gov/servlets/purl/1833697.
@article{osti_1833697,
title = {Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas},
author = {Hickman, Alison B. and Kailasan, Shweta and Genzor, Pavol and Haase, Astrid D. and Dyda, Fred},
abstractNote = {Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that the Methanosarcina mazei casposase can integrate varied forms of the casposon end in vitro, and recapitulates several properties of CRISPR-Cas integrases including site-specificity. The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization; this in turn led to preferred integration of single spacers over two transposon ends.},
doi = {10.7554/elife.50004},
journal = {eLife},
number = ,
volume = 9,
place = {United States},
year = {Wed Jan 08 00:00:00 EST 2020},
month = {Wed Jan 08 00:00:00 EST 2020}
}
Works referenced in this record:
How type II CRISPR–Cas establish immunity through Cas1–Cas2-mediated spacer integration
journal, September 2017
- Xiao, Yibei; Ng, Sherwin; Nam, Ki Hyun
- Nature, Vol. 550, Issue 7674
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity
journal, May 2014
- Krupovic, Mart; Makarova, Kira S.; Forterre, Patrick
- BMC Biology, Vol. 12, Issue 1
Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back
journal, September 2017
- Koonin, Eugene V.; Makarova, Kira S.
- Genome Biology and Evolution, Vol. 9, Issue 10
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Spacer capture and integration by a type I-F Cas1–Cas2-3 CRISPR adaptation complex
journal, June 2017
- Fagerlund, Robert D.; Wilkinson, Max E.; Klykov, Oleg
- Proceedings of the National Academy of Sciences
Adaptation in CRISPR-Cas Systems
journal, March 2016
- Sternberg, Samuel H.; Richter, Hagen; Charpentier, Emmanuelle
- Molecular Cell, Vol. 61, Issue 6
Structures of the CRISPR genome integration complex
journal, July 2017
- Wright, Addison V.; Liu, Jun-Jie; Knott, Gavin J.
- Science, Vol. 357, Issue 6356
The mechanism of retroviral integration from X-ray structures of its key intermediates
journal, November 2010
- Maertens, Goedele N.; Hare, Stephen; Cherepanov, Peter
- Nature, Vol. 468, Issue 7321
Quantitative mass imaging of single biological macromolecules
journal, April 2018
- Young, Gavin; Hundt, Nikolas; Cole, Daniel
- Science, Vol. 360, Issue 6387
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
journal, March 2007
- Barrangou, R.; Fremaux, C.; Deveau, H.
- Science, Vol. 315, Issue 5819
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0
journal, October 2003
- Bricogne, G.; Vonrhein, C.; Flensburg, C.
- Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11
Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems
journal, September 2016
- Béguin, Pierre; Charpin, Nicole; Koonin, Eugene V.
- Nucleic Acids Research
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
journal, November 2015
- Shmakov, Sergey; Abudayyeh, Omar O.; Makarova, Kira S.
- Molecular Cell, Vol. 60, Issue 3, p. 385-397
Foreign DNA capture during CRISPR–Cas adaptive immunity
journal, October 2015
- Nuñez, James K.; Harrington, Lucas B.; Kranzusch, Philip J.
- Nature, Vol. 527, Issue 7579
Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007
- Krissinel, Evgeny; Henrick, Kim
- Journal of Molecular Biology, Vol. 372, Issue 3
Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems
journal, August 2016
- Mohanraju, Prarthana; Makarova, Kira S.; Zetsche, Bernd
- Science, Vol. 353, Issue 6299
A Functional Mini-Integrase in a Two-Protein Type V-C CRISPR System
journal, February 2019
- Wright, Addison V.; Wang, Joy Y.; Burstein, David
- Molecular Cell, Vol. 73, Issue 4
Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition
journal, August 2015
- Rollie, Clare; Schneider, Stefanie; Brinkmann, Anna Sophie
- eLife, Vol. 4
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons
journal, May 2005
- Kapitonov, Vladimir V.; Jurka, Jerzy
- PLoS Biology, Vol. 3, Issue 6
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems
journal, November 2015
- Wang, Jiuyu; Li, Jiazhi; Zhao, Hongtu
- Cell, Vol. 163, Issue 4
CRISPR–Cas adaptation: insights into the mechanism of action
journal, January 2016
- Amitai, Gil; Sorek, Rotem
- Nature Reviews Microbiology, Vol. 14, Issue 2
The Mu transpososome structure sheds light on DDE recombinase evolution
journal, November 2012
- Montaño, Sherwin P.; Pigli, Ying Z.; Rice, Phoebe A.
- Nature, Vol. 491, Issue 7424
Characterizing leader sequences of CRISPR loci
journal, September 2016
- Alkhnbashi, Omer S.; Shah, Shiraz A.; Garrett, Roger A.
- Bioinformatics, Vol. 32, Issue 17
Prespacer processing and specific integration in a Type I-A CRISPR system
journal, December 2017
- Rollie, Clare; Graham, Shirley; Rouillon, Christophe
- Nucleic Acids Research, Vol. 46, Issue 3
Sequence motifs recognized by the casposon integrase of Aciduliprofundum boonei
journal, May 2019
- Béguin, Pierre; Chekli, Yankel; Sezonov, Guennadi
- Nucleic Acids Research, Vol. 47, Issue 12
New insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination
journal, January 2017
- Carmona, Lina Marcela; Schatz, David G.
- The FEBS Journal, Vol. 284, Issue 11
Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity
journal, January 2016
- Krupovic, Mart; Shmakov, Sergey; Makarova, Kira S.
- Genome Biology and Evolution, Vol. 8, Issue 2
Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity
journal, May 2014
- Nuñez, James K.; Kranzusch, Philip J.; Noeske, Jonas
- Nature Structural & Molecular Biology, Vol. 21, Issue 6
CRISPR Immunological Memory Requires a Host Factor for Specificity
journal, June 2016
- Nuñez, James K.; Bai, Lawrence; Harrington, Lucas B.
- Molecular Cell, Vol. 62, Issue 6
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
Transposases are the most abundant, most ubiquitous genes in nature
journal, March 2010
- Aziz, Ramy K.; Breitbart, Mya; Edwards, Robert A.
- Nucleic Acids Research, Vol. 38, Issue 13
Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense
journal, June 2009
- Wiedenheft, Blake; Zhou, Kaihong; Jinek, Martin
- Structure, Vol. 17, Issue 6
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications
journal, November 2015
- Hickman, Alison B.; Dyda, Fred
- Nucleic Acids Research, Vol. 43, Issue 22
Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?
journal, October 2018
- Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.
- The CRISPR Journal, Vol. 1, Issue 5
CRISPR-Cas: Adapting to change
journal, April 2017
- Jackson, Simon A.; McKenzie, Rebecca E.; Fagerlund, Robert D.
- Science, Vol. 356, Issue 6333
Version 1.2 of the Crystallography and NMR system
journal, October 2007
- Brunger, Axel T.
- Nature Protocols, Vol. 2, Issue 11
Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection
journal, January 2008
- Barabas, Orsolya; Ronning, Donald R.; Guynet, Catherine
- Cell, Vol. 132, Issue 2
Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery
journal, August 2017
- Krupovic, Mart; Béguin, Pierre; Koonin, Eugene V.
- Current Opinion in Microbiology, Vol. 38
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
Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity
journal, November 2013
- Kim, Tae-Yang; Shin, Minsang; Huynh Thi Yen, Ly
- Biochemical and Biophysical Research Communications, Vol. 441, Issue 4
V(D)J Recombination: Mechanisms of Initiation
journal, December 2011
- Schatz, David G.; Swanson, Patrick C.
- Annual Review of Genetics, Vol. 45, Issue 1
CRISPR-Cas immunity in prokaryotes
journal, October 2015
- Marraffini, Luciano A.
- Nature, Vol. 526, Issue 7571
Molecular mechanisms of CRISPR–Cas spacer acquisition
journal, August 2018
- McGinn, Jon; Marraffini, Luciano A.
- Nature Reviews Microbiology, Vol. 17, Issue 1
Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein
journal, February 2016
- Silas, S.; Mohr, G.; Sidote, D. J.
- Science, Vol. 351, Issue 6276
CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration
journal, November 2016
- McGinn, Jon; Marraffini, Luciano A.
- Molecular Cell, Vol. 64, Issue 3
CRISPR–Cas in mobile genetic elements: counter-defence and beyond
journal, June 2019
- Faure, Guilhem; Shmakov, Sergey A.; Yan, Winston X.
- Nature Reviews Microbiology, Vol. 17, Issue 8
New CRISPR–Cas systems from uncultivated microbes
journal, December 2016
- Burstein, David; Harrington, Lucas B.; Strutt, Steven C.
- Nature, Vol. 542, Issue 7640
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Apollo - University of Cambridge Repository
Overview of the CCP4 suite and current developments.
text, January 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Apollo - University of Cambridge Repository
Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection
journal, January 2008
- Barabas, Orsolya; Ronning, Donald R.; Guynet, Catherine
- Cell, Vol. 132, Issue 2
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems
journal, November 2015
- Wang, Jiuyu; Li, Jiazhi; Zhao, Hongtu
- Cell, Vol. 163, Issue 4
Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery
journal, August 2017
- Krupovic, Mart; Béguin, Pierre; Koonin, Eugene V.
- Current Opinion in Microbiology, Vol. 38
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
journal, November 2015
- Shmakov, Sergey; Abudayyeh, Omar O.; Makarova, Kira S.
- Molecular Cell, Vol. 60, Issue 3, p. 385-397
Adaptation in CRISPR-Cas Systems
journal, March 2016
- Sternberg, Samuel H.; Richter, Hagen; Charpentier, Emmanuelle
- Molecular Cell, Vol. 61, Issue 6
CRISPR Immunological Memory Requires a Host Factor for Specificity
journal, June 2016
- Nuñez, James K.; Bai, Lawrence; Harrington, Lucas B.
- Molecular Cell, Vol. 62, Issue 6
CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration
journal, November 2016
- McGinn, Jon; Marraffini, Luciano A.
- Molecular Cell, Vol. 64, Issue 3
Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense
journal, June 2009
- Wiedenheft, Blake; Zhou, Kaihong; Jinek, Martin
- Structure, Vol. 17, Issue 6
Advances in direct methods for protein crystallography
journal, October 1999
- Usón, Isabel; Sheldrick, George M.
- Current Opinion in Structural Biology, Vol. 9, Issue 5
The mechanism of retroviral integration from X-ray structures of its key intermediates
journal, November 2010
- Maertens, Goedele N.; Hare, Stephen; Cherepanov, Peter
- Nature, Vol. 468, Issue 7321
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
CRISPR-Cas immunity in prokaryotes
journal, October 2015
- Marraffini, Luciano A.
- Nature, Vol. 526, Issue 7571
Foreign DNA capture during CRISPR–Cas adaptive immunity
journal, June 2016
- Nuñez, James K.; Harrington, Lucas B.; Kranzusch, Philip J.
- Nature, Vol. 534, Issue 7607
New CRISPR–Cas systems from uncultivated microbes
journal, December 2016
- Burstein, David; Harrington, Lucas B.; Strutt, Steven C.
- Nature, Vol. 542, Issue 7640
How type II CRISPR–Cas establish immunity through Cas1–Cas2-mediated spacer integration
journal, September 2017
- Xiao, Yibei; Ng, Sherwin; Nam, Ki Hyun
- Nature, Vol. 550, Issue 7674
Version 1.2 of the Crystallography and NMR system
journal, October 2007
- Brunger, Axel T.
- Nature Protocols, Vol. 2, Issue 11
CRISPR–Cas adaptation: insights into the mechanism of action
journal, January 2016
- Amitai, Gil; Sorek, Rotem
- Nature Reviews Microbiology, Vol. 14, Issue 2
Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity
journal, May 2014
- Nuñez, James K.; Kranzusch, Philip J.; Noeske, Jonas
- Nature Structural & Molecular Biology, Vol. 21, Issue 6
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion
journal, September 2020
- Benton, Donald J.; Wrobel, Antoni G.; Xu, Pengqi
- Nature, Vol. 588, Issue 7837
The basic building blocks and evolution of CRISPR–Cas systems
journal, November 2013
- Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.
- Biochemical Society Transactions, Vol. 41, Issue 6
Spacer capture and integration by a type I-F Cas1–Cas2-3 CRISPR adaptation complex
journal, June 2017
- Fagerlund, Robert D.; Wilkinson, Max E.; Klykov, Oleg
- Proceedings of the National Academy of Sciences
Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?
journal, October 2018
- Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.
- The CRISPR Journal, Vol. 1, Issue 5
Characterizing leader sequences of CRISPR loci
journal, September 2016
- Alkhnbashi, Omer S.; Shah, Shiraz A.; Garrett, Roger A.
- Bioinformatics, Vol. 32, Issue 17
Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity
journal, January 2016
- Krupovic, Mart; Shmakov, Sergey; Makarova, Kira S.
- Genome Biology and Evolution, Vol. 8, Issue 2
Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back
journal, September 2017
- Koonin, Eugene V.; Makarova, Kira S.
- Genome Biology and Evolution, Vol. 9, Issue 10
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
The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications
journal, November 2015
- Hickman, Alison B.; Dyda, Fred
- Nucleic Acids Research, Vol. 43, Issue 22
Sequence motifs recognized by the casposon integrase of Aciduliprofundum boonei
journal, May 2019
- Béguin, Pierre; Chekli, Yankel; Sezonov, Guennadi
- Nucleic Acids Research, Vol. 47, Issue 12
Zero-dose extrapolation as part of macromolecular synchrotron data reduction
journal, April 2003
- Diederichs, Kay; McSweeney, Sean; Ravelli, Raimond B. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 5
New insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination
journal, January 2017
- Carmona, Lina Marcela; Schatz, David G.
- The FEBS Journal, Vol. 284, Issue 11
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
journal, March 2007
- Barrangou, R.; Fremaux, C.; Deveau, H.
- Science, Vol. 315, Issue 5819
Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein
journal, February 2016
- Silas, S.; Mohr, G.; Sidote, D. J.
- Science, Vol. 351, Issue 6276
Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems
journal, August 2016
- Mohanraju, Prarthana; Makarova, Kira S.; Zetsche, Bernd
- Science, Vol. 353, Issue 6299
CRISPR-Cas: Adapting to change
journal, April 2017
- Jackson, Simon A.; McKenzie, Rebecca E.; Fagerlund, Robert D.
- Science, Vol. 356, Issue 6333
Structures of the CRISPR genome integration complex
journal, July 2017
- Wright, Addison V.; Liu, Jun-Jie; Knott, Gavin J.
- Science, Vol. 357, Issue 6356
Everyman's Guide to Bacterial Insertion Sequences
journal, April 2015
- Siguier, Patricia; Gourbeyre, Edith; Varani, Alessandro
- Microbiology Spectrum, Vol. 3, Issue 2
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons
journal, May 2005
- Kapitonov, Vladimir V.; Jurka, Jerzy
- PLoS Biology, Vol. 3, Issue 6
Works referencing / citing this record:
The CARF Protein MM_0565 Affects Transcription of the Casposon-Encoded cas1-solo Gene in Methanosarcina mazei Gö1
journal, August 2020
- Ulbricht, Andrea; Nickel, Lisa; Weidenbach, Katrin
- Biomolecules, Vol. 10, Issue 8