Table 1.
Main CRISPR-Cas systems subtypes and examples of system-harboring microorganisms and clostridial species.
| Class | Subtype | cas operon composition | Example | Examples of clostridial species and strains |
|---|---|---|---|---|
| Class 1 | I-A | cas6, cas11(csa5), cas7, cas5, cas8a1, cas3’, cas3”, cas2, cas4, cas1, cas4 | Listeria monocytogenes L99 (Sesto et al., 2014) | C. stercorarium subsp. stercorarium DSM 8532 (Poehlein et al., 2013); C. tetani ATCC 9441 (Cohen et al., 2017) |
| I-B | cas6, cas8b1, cas7, cas5, cas3, cas4, cas1, cas2 | Haloferax volcanii H119 (Maier et al., 2013b) | C. difficile 630, C. difficile R20291 (Boudry et al., 2015); C. pasteurianum BC1 (Pyne et al., 2016); C. acetobutylicum GXAS18-1 (Peng et al., 2014); C. tetani ATCC 9441 (Cohen et al., 2017) | |
| I-C | cas3, cas5, cas8c, cas7, cas4, cas1, cas2 | Desulfovibrio vulgaris str. Hildenborough (Hochstrasser et al., 2016) | C. cellulolyticum H10 (Brown et al., 2014) | |
| I-U | cas3, cas8u2, cas7, cas5-cas6, cas4-cas1, cas2 | Geobacter sulfurreducens (Koonin et al., 2017) | – | |
| I-D | cas3’, cas3”, cas10d, cas7(csc2), cas5(csc1), cas6, cas4, cas1, cas2 | Cyanothece sp. 8802 (Koonin et al., 2017) | – | |
| I-E | cas3, cas8e(cse1), cas11(cse2), cas7, cas5, cas6, cas1, cas2 | Escherichia coli K12 (Koonin et al., 2017) | – | |
| I-F | cas1, cas2-cas3, cas8f(csy1), cas5(csy2), cas7(csy3), cas6f | Pseudomonas aeruginosa PA14 (Wiedenheft et al., 2011) | – | |
| III-A | cas6, cas10, cas11(csm2), cas7(csm3), cas5(csm4), cas7(csm5), csm6, cas1, cas2 | Staphylococcus epidermidis (Koonin et al., 2017) | C. tetani ATCC 453 (Cohen et al., 2017) | |
| III-B | cas7(cmr1), cas10, cas5(cmr3), cas7(cmr4), cas11(cmr5), cas6, cas7(cmr6) | Pyrococcus furiosus (Koonin et al., 2017) | C. botulinum ATCC 3502 (Negahdaripour et al., 2017) | |
| III-C | cas7(cmr1), cas7(cmr6), cas10, cas7(cmr4), cas11(cmr5), cas5(cmr3) | Methanothermobacter thermautotrophicus (Koonin et al., 2017) | – | |
| III-D | cas10, cas7(csm3), cas5(csx10), cas11(csm2), cas7(csm7), cas7(csm5), all1473, cas7(csm5) | Synechocystis sp. 6803 (Makarova et al., 2015) | – | |
| Class 2 | II-A | cas9, cas1, cas2, csn2 | Enterococcus faecalis OG1RF (Bourgogne et al., 2008) | – |
| II-B | cas9, cas1, cas2, cas4 | Legionella pneumophila str. Paris (Koonin et al., 2017) | – | |
| II-C | cas9, cas1, cas2 | Neisseria lactamica 020-06 (Koonin et al., 2017) | C. perfringens JGS1495 (Pearson et al., 2015) | |
| V-A | cas12a(cpf1), cas4, cas1, cas2 | Francisella cf. novicida Fx1 (Koonin et al., 2017) | – | |
| V-B | cas12b(c2c1), cas4, cas1, cas2 | Alicyclobacillus acidoterrestris (Koonin et al., 2017) | – | |
| V-C | cas1, cas12c(c2c3) | Oleiphilus sp. (Koonin et al., 2017) | – | |
| V-D | cas1, cas12d(casY) | Bacterium CG09_39_24 (Koonin et al., 2017) | – | |
| V-E | cas12e(casX), cas4, cas1, cas2 | Deltaproteobacteria bacterium (Koonin et al., 2017) | – | |
CRISPR-Cas systems subtypes and the composition of cas operons are shown according to classification of Koonin et al. (2017). Fused cas genes in operons are marked with a dash.