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

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]