Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.
Highlights
Cas2 is universally conserved and essential for new CRISPR spacer acquisition
Metal-dependent Double-stranded Nuclease Activity in B. halodurans Cas2—Non-homologous recombination in CRISPR-cas system has been suggested for new spacer acquisition [33]
A genetic study revealed that Cas1 or Cas2 proteins are required for the new spacer acquisition [8]
Summary
Cas is universally conserved and essential for new CRISPR spacer acquisition. Results: Bha_Cas uses a single metal ion to cleave dsDNA and is likely activated by a pH-dependent conformational change. Cas is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. We show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA This activity is consistent with its putative function in producing new spacers for insertion into the 5-end of the CRISPR locus. Our assay revealed that Bha_Cas is a metal-dependent double-stranded (ds)DNA endonuclease instead of an RNase This conclusion was further strengthened by the identification of dsDNase activities in the Thermus thermophilus Cas (Tth_Cas2) protein from another CRISPR subtype. These together with the observation that the dsDNase activity and metal chelation in Bha_Cas are strongly correlated and steeply pH-dependent, point to the possibility that a pH-dependent conformational change enables the Bha_Cas protein to chelate a divalent metal ion in the active site, which in turn enables the protein to cleave dsDNA
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