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Table 2 Applications of type II CRISPR/Cas systems in bacteria, including genome editing, transcriptional regulation and base editors

From: Application of different types of CRISPR/Cas-based systems in bacteria

Cas protein Target species Strategy and type of modifications References
Sp Cas9 Actinomycetes Genome editing, deletion and replacement [58]
Sp Cas9 Actinoplanes sp. Genome editing, deletion [46]
Sp Cas9 B. subtilis Genome editing, deletions (25.1 kb and 4.1 kb) [40]
Sp Cas9 B. subtilis Genome editing, gene disruption (33 to 53%) [47]
Sp Cas9 C. acetobutylicum Genome editing, deletions and insertions (3.6 kb) [41]
Sp Cas9 C. acetobutylicum Genome editing, deletion and replacement [44]
Sp Cas9 C. autoethanogenum Genome editing, deletions (over 50% when screening a small library of tetracycline-inducible promoters) [56]
Sp Cas9 C. beijerinckii Genome editing, deletion and integration in single steps [51]
Sp Cas9 C. difficile Genome editing, site-specific mutations (20–50%) [54]
Sp Cas9 C. glutamicum Genome editing, deletion, point mutations and insertion (up to 100%) [50]
Sp Cas9 C. glutamicum Genome editing, knockout and GABA overproduction [48]
Sp Cas9 C. glutamicum Genome editing, deletion (60%) and insertion (62.5%) [49]
Sp Cas9 C. saccharoperbutylacetonicum Genome editing, deletions (75%) [55]
Sp Cas9 E. coli Genome editing, knockouts, insertions or substitutions (100%, 5 days) [28]
Sp Cas9 E. coli Genome editing, point mutations, deletions, and insertions [29]
Sp Cas9 E. coli Genome editing, knock-in [30]
Sp Cas9 E. coli Genome editing, knockout (100%, 3 days) [31]
Sp Cas9 E. coli Genome editing, (3 genes between 96.5 and 99.7%) [33]
Sp Cas9 E. coli Genome editing, deletions, insertions, and replacements (100%) [35]
Sp Cas9 E. coli Genome editing, deletion (19.4 kb) and insertion (3 kb) [37]
Sp Cas9 E. coli Genome editing, deletion (large chromosomal DNA fragments) [57]
Sp Cas9 E. coli Genome editing, insertion (70 to 100%) [38]
Sp Cas9 E. coli Genome editing, replacement (99%) and insertion (2.4 kb 91%, 3.9 kb 92%, 5.4 kb 71%, and 7.0 kb 61%) [39]
Sp Cas9 S. aureus Genome editing, knockout, knock-in and single base mutations [32]
Sp Cas9 S. coelicolor Genome editing, deletion (939 bp) [53]
Sp Cas9 S. coelicolor Genome editing, single gene deletion, single large-size gene cluster deletion (60% to 100%), simultaneous deletions of actII-orf4 and redD, as well as the ACT and RED biosynthetic gene clusters with high efficiencies of 54 and 45%, respectively. [34]
Sp Cas9 S. elongatus Genome editing, deletion (100%) [45]
Sp Cas9 Streptomyces Multiple genome editing, deletions (from 20 bp to 30 kb, 70 to 100%) [42]
Sp Cas9 Streptomyces Multiple genome editing, knock-in (5 species) [43]
Sp Cas9 S. rimosus Genome editing, deletions (100%) and point mutations [52]
Thermo Cas9 B. smithii Genome editing, knockouts and silencing (55 °C) [36]
Sp nCas9 B. licheniformis Genome editing, deletions (1 gene 100%, 2 genes 11.6%, large-fragment 79%) and insertions (76.5%) [61]
Sp nCas9 C. perfringens Genome editing, deletion (23 bp) [62]
Sp nCas9 (D10A) E. coli Genome editing, deletions (from 36 to 96 kb) [17]
Sp nCas9 (D10A) L. casei Genome editing, deletions and insertions (25 to 62%) [59]
Sp dCas9 B. subtilis CRISPRi, investigation of gene function (289 known or proposed essential genes, ~ 94% successfully targeting of bona fide essential genes) [69]
Sp dCas9 C. glutamicum CRISPRi (single gene, two genes) [63]
Sp dCas9 C. acetobutylicum CRISPRi [60]
Sp dCas9 C. beijerinckii CRISPRi (97%) [64]
Sp dCas9 E. coli CRISPRi [23]
Sp dCas9 E. coli CRISPRi (1000-fold repression) [24]
Sp dCas9 E. coli CRISPRi (10-fold repression) [21]
Sp dCas9 E. coli CRISPRi [22]
Sp dCas9 E. coli CRISPRi, investigation of gene function [68]
Sp dCas9 E. coli CRISPRi, harboring a biosynthetic mevalonate (MVA) pathway and enhancing production of (-)-α-bisabolol (C15) and lycopene (C40) [71]
Sp dCas9 E. coli CRISPRi, pinosylvin biosynthesis by inactivating a malonyl-CoA depleting pathway and a 1.9-fold increase of the pinosylvin content [73]
Sp dCas9 E. coli CRISPRi, pinosylvin synthesis pathway and the final pinosylvin titer was improved to 281 mg/L, which was the highest pinosylvin titer [119]
Sp dCas9 E. coli CRISPRi, the methionine biosynthetic pathway and a final titer of 51 mg/L(21-fold improvement overall) [74]
Sp dCas9 E. coli CRISPRi, malate biosynthetic pathway and 2.3-fold increase in malate titer [75]
Sp dCas9 E. coli CRISPRi, multiplex repression of competing pathway and n‑butanol yield and productivity increased up to 5.4‑ and 3.2‑fold, respectively. [76]
Sp dCas9 E. coli CRISPRi, downregulate fatty acid biosynthesis pathway to inactivate the malonyl-CoA consumption pathway [77]
Sp dCas9 E. coli CRISPRi, 1,4-BDO production and enhanced the 1,4-BDO titer for 100% to 1.8 g/L [78]
Sp dCas9 E. coli CRISPRi, the butanol synthetic pathway and 0.82 g/L butanol production [79]
Sp dCas9 E. coli CRISPRi, the biological synthesis of polyketides, flavonoids and biofuels and 7.4-fold higher production [80]
Sp dCas9 M. tuberculosis CRISPRi [67]
Sp dCas9 M. tuberculosis CRISPRi, single or multiple targets [66]
Sp dCas9 Pseudomonas spp. CRISPRi [20]
Sp dCas9 B. melitensis Base editor (C-T, 100%) [26]
Sp dCas9 C. glutamicum Base editor, (single-locus, 100%, double-locus, 87.2%, and triple-locus, 23.3%) [85]
Sp dCas9 E. coli Base editor (C-T, 99.93%) [26]
Sp dCas9 K. pneumoniae Base editor (position, PAM distal 4 to 8 bp, efficiency 100%) [87]
Sp dCas9 Staphylococcus Base editor (position, PAM distal 4 to 8 bp, efficiency 100%) [88]