Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a

CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here th...

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Bibliographic Details
Published in:eLife 2019-08, Vol.8
Main Authors: Knott, Gavin J, Cress, Brady F, Liu, Jun-Jie, Thornton, Brittney W, Lew, Rachel J, Al-Shayeb, Basem, Rosenberg, Daniel J, Hammel, Michal, Adler, Benjamin A, Lobba, Marco J, Xu, Michael, Arkin, Adam P, Fellmann, Christof, Doudna, Jennifer A
Format: Article
Language:English
Subjects:
Acidaminococcus - enzymology
Acidaminococcus - virology
anti-CRISPR
Bacteria
bacteriophage
Bacteriophages
Bacteriophages - growth & development
BASIC BIOLOGICAL SCIENCES
Biochemistry
Biochemistry and Chemical Biology
Cells (Biology)
Clostridiales - enzymology
Clostridiales - virology
Coevolution
CRISPR-Cas
CRISPR-Cas Systems - drug effects
DNA
DNA binding
Enzyme inhibitors
Enzyme Inhibitors - metabolism
Enzymes
Evolution, Molecular
Genomes
Genomics
Host-Parasite Interactions
Microbiology
Natural history
Physiological aspects
Prevention
Transposons
Viral Proteins - metabolism
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Summary:CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here that the inhibitor AcrVA4 uses a previously undescribed strategy to recognize the Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. The Cas12a (AsCas12a) enzyme, widely used for genome editing applications, contains an ancestral helical bundle that blocks AcrVA4 binding and allows it to escape anti-CRISPR recognition. Using biochemical, microbiological, and human cell editing experiments, we show that Cas12a orthologs can be rendered either sensitive or resistant to AcrVA4 through rational structural engineering informed by evolution. Together, these findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.49110