TABLE 3.
Previous genome reduced bacterial strains.
| Strain | Deletion | Deletion size | Deletion method | Characteristics (relative to parental strain) | References |
|---|---|---|---|---|---|
| Bacillus amyloliquefaciens | |||||
| GR167 | Genomic islands, extracellular polysaccharide biosynthesis genes, prophages | 167 Kb (4.18%) | HR with upp CS | Faster growth, higher transformation efficiency, increased heterologous gene expression | Zhang et al. (2020) |
| Bacillus subtilis | |||||
| ∆6 | Prophages, pks operon | 323 Kb (7.7%) | HR with no CS | Comparable growth rate | Westers et al. (2003) |
| MG1M | Prophages, antibiotic production genes | 991 Kb (24%) | HR | Reduced growth rate, unstable recombinant protein production | Ara et al. (2007) |
| MGB874 | 74 regions including prophages, secondary metabolite producing genes, etc | 873.5 Kb (20.7%) | HR with upp CS | Increase in cellulase (1.7-fold) and protease (2.5-fold) production | Morimoto et al. (2008) |
| BSK814G2 | Prophages, antibiotic production operons and other nonessential regions | 814 Kb (20%) | HR with upp CS | Decreased growth characteristics but 4.4-fold higher guanosine production | Li et al. (2016b) |
| BSK756T3 | Prophages, antibiotic production operons and other nonessential regions | 756 Kb (18.6%) | HR with upp CS | Decreased growth characteristics but 5.2-fold higher thymidine production | Li et al. (2016b) |
| PG10 | Many genes including those for sporulation, motility, secondary metabolism, prophages, secreted proteases, etc. | 1.46 Mb (36%) | HR with manP CS | Decreased growth rate, lower resource utilization for information processing, improved production of ‘difficult proteins’ that cannot be produced in other Bacillus subtilis strains | Reuß et al. (2017) |
| Suárez et al. (2019) | |||||
| Corynebacterium glutamicum | |||||
| MB001 | 3 Prophages | 204.7 Kb (6%) | HR with SacB CS | Improved growth under stress conditions, increased transformation efficiency, 30% increase in heterologous protein production | Baumgart et al. (2013) |
| C1* | Non-essential genes including prophages, unknown genesetc. | 440 Kb (13.4%) | HR with sacB CS | Robust against stresses, improved growth stability, similar growth rates | Baumgart et al. (2018) |
| CR101 | All prophages and IS elements | 249.4 Kb (7.6%) | HR with sacB CS | Similar growth rate and transformation efficiency to MB001 | Linder et al. (2021) |
| Escherichia coli | |||||
| MDS42 | Insertion sequences | 663.3 Kb (14.3%) | λ-Red HR with I-SceI + P1 transduction | Improved electroporation efficiency, similar growth rates | Pósfai et al. (2006) |
| ∆16 | Various deletions across the E. coli genome | 1.38 Mb (29.7%) | λ-Red HR with sacB and rpsL CS + P1 transduction | Slower growth and abnormal cell morphology | Hashimoto et al. (2005) |
| MGF-01 | Various nonessential gene regions | 1.03 Mb (22%) | λ-Red HR + P1 transduction | 1.5-fold higher cell density and 2x threonine production from an introduced gene cassette | Mizoguchi et al. (2007) |
| MS56 | IS Elements, K-islands, flagella genes, LPS synthesis genes | 1.1 Mb (23%) | λ-Red HR with I-SceI + sacB CS | 1.6-fold faster growth and improved genomic stability | Park et al. (2014) |
| Lactococcus lactis | |||||
| 9K-4 | Prophages, integrases, and transposases | 71 Kb (2.83%) | Cre-LoxP | Faster growth rate, increased biomass yield, improved heterologous gene expression 3-4-fold | Zhu et al. (2017) |
| N8-8 | Prophages and genomic islands | 176 Kb (6.86%) | Cre-LoxP | Shortened generation time by 17%, similar nisin yield | Qiao et al. (2022) |
| Magnetospirillum gryphiswaldense | |||||
| ∆TZ-17 | Prophages, transposases, nitrogen fixation genes, pks operon | 227 Kb (5.5%) | HR with galK CS | Comparable growth rate and magnetosome biosynthesis with improved genomic stability | Zwiener et al. (2021) |
| Mycoplasma mycoides | |||||
| JCVI-syn3A | All nonessential or quasi essential genes | 669 Kb (55.2%) | Chemical synthesis | Improved growth rates compared to JCVI-syn3.0 | Breuer et al. (2019) |
| Pseudomonas alloputida | |||||
| KTU-13 | Genomic islands | 254.5 Kb (4.1%) | HR with sacB CS | 45-fold increase in transformation efficiency, 9.4-fold increase in heterologous protein expression, 39% increase in PHA production | Liang et al. (2020) |
| EM383 | Flagellar biosynthesis genes, prophages, transposases, recombinases | 265.8 Kb (4.3%) | HR with ISce-I | Improved growth rate, heterologous protein expression, plasmid stability, stress resistance, and more | Lieder et al. (2015) |
| Martínez-García et al. (2014) | |||||
| Pseudomonas mendocina | |||||
| NKU421 | Genomic island, prophages, hypothetical protein clusters | 418 Kb (7.7%) | HR with upp CS | Increased ATP/ADP ratio by 11x, Improved mcl-PHA and alginate oligosaccharide production by 114.8 and 27.8% respectively | Fan et al. (2020) |
| Pseudomonas taiwanesis | |||||
| VBL120 | Megaplasmid, prophages, flagellar biosynthesis genes, and biofilm genes | 640 Kb (10.7%) | I-SceI HR with CS | Increased growth rates and biomass yield, improved production of chemicals including phenol | Wynands et al. (2019) |
| Sinorhizobium meliloti | |||||
| Rm1021 | 2 megaplasmids containing nonessential genes including toxin/antitoxin systems | 3.1 Mb (46%) | Flp/FRT | Identification of 4 toxin/antitoxin pairs that are essential | Milunovic et al. (2014) |
| Streptomyces albus | |||||
| J1074 (Del14) | 15 biosynthetic secondary metabolite gene clusters | 500 Kb (7.3%) | HR of mutant BAC library and phiC31 integrase | Comparable growth rates and improved heterologous gene expression of 7 products by 2–2.4 fold | Myronovski et al. (2018) |
| Streptomyces avermitilis | |||||
| SUKA17 | Biosynthetic genes, prophages, transposases | 1.67 Mb (18.5%) | Cre/LoxP | Increased streptomycin (4-fold) and cephamycin C (2-fold) production | Komatsu et al. (2010) |
| Streptomyces chattanoogensis | |||||
| L321 | Biosynthetic clusters including the natamycin biosynthetic cluster | 700 Kb (7.7%) | Cre/LoxP | Increased ATP and NADPH availability, higher transformation efficiency, improved heterologous gene expression, and increased genetic stability | Bu et al. (2019) |