Table 1 Comparison of three types of CRISPR-Cas systems

  Whether to depend on PAM when selecting proto-spacers

Yes

Yes

No

  Pre-crRNA conjugates

Cascade complex

Cas9 (Csn1/Csx12) tracrRNA

Cas6

Csm (subtype III-A)/

Cmr (subtype III-B)^a

  Pre-crRNA cleavage enzymes

Cas6e subunit (subtype I-E)/Cas6f subunit (subtype I-F)

Housekeeping RNase III

Cas6

  Processes to mature crRNA

1. A typical 8-nucleotide repeat fragment on the 5′ end

2. A hairpin structure on the 3′ flank

Cleavage at a fixed distance within the spacers (probably catalyzed by Cas9)

1. Cas6 is responsible for the processing step

2. Trimming the 3′ end of the crRNA further (Nucleases have not yet been identified.)

  Methods of target recognition

Cascade complex guided by crRNA

Cas9 loaded with crRNA directly

The invading DNA fragment having no base pairing to the 5′ repeat fragment of the mature crRNA (resulting in interference)

  Targets cleavage enzymes

Cas3

Cas9

Cas6 or Cmr/Csm complex

  Targets

DNA

DNA

DNA (III-A)/

RNA (III-B)

  Whether to depend on PAM to cleaving process

Yes

Yes

No

Special systems contained

cas3 gene

‘HNH’-type system

Polymerase and RAMP modules

Distribution of the three types of CRISPR-Cas systems

More common in Archaea

Only in Bacteria

More common in Archaea