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. 2023 Apr 8;14:1984. doi: 10.1038/s41467-023-37748-7

Table 1.

Top-down genome minimisation projects

Parental strain and size Designation and size Minimisation method Size/ Percentage of reduction Phenotypes of the resulting strains Applications Refs
Escherichia coli W3110 4.65 Mb E. coli MGF-01 3.62 Mb Lambda homologous recombination and P1 transduction 1030 kb (22.2%) Improved growth in M9 minimal medium Enhanced threonine production 11,15
Escherichia coli W3110 4.65 Mb E. coli DGF-298 2.98 Mb Lambda homologous recombination and P1 transduction 1670 kb (35.9%) Better growth fitness and cell yield in a rich medium N/A 16
Escherichia coli MG1655 4.64 Mb E. coli CDΔ3456 4.33 Mb Tn5-targeted Cre/loxP excision and P1 transduction 313.1 kb (6.7%) Normal growth in LB broth N/A 9
Escherichia coli MG1655 4.64 Mb E. coli △16 3.26 Mb Lambda homologous recombination and P1 transduction 1377.2 kb (29.7%) Much slower growth rate, longer and wider cell shape than the parental strain, abnormal nucleoid organisation N/A 17
Escherichia coli MG1655 4.64 Mb E. coli △33a 2.83 Mb Homologous recombination and FLP-FRT site-specific recombination and P1 transduction 1806.6 kb (38.9%) Sensitive to oxidative stress N/A 18
Bacillus subtilis 168 4.22 Mb B. subtilis Δ6 3.9 Mb Homologous recombination and excision 320 kb (7.7%) Normal growth, intracellular carbon metabolism, competence and sporulation, but changed motility No significant difference of α-amylase (AmyQ) secretion compared to the wild-type 10
Bacillus subtilis 168 4.22 Mb B. subtilis PG10 2.76 Mb and PS38 2.68 Mb Homologous recombination and counter selection PG10 1.46 Mb (36%) PS38 1.54 Mb (36.5%) Comparable growth to the wild- type in complex medium PG10 showed substantially higher capacity for protein secretion 20,54
Streptomyces avermitilis 9.02 Mb S. avermitilis SUKA 7.35–7.51 Mb Homologous recombination and Cre-mediated recombination 1.52–1.67 Mb (16.9–18.54%) Could grow on the minimum medium Higher streptomycin and cephamycin C production than their native hosts; produce the plant terpenoid Intermediate, amorpha-4,11-diene, successfully 12
Schizosaccharomyces pombe 12.09 Mb S. pombe A8 11.43 Mb Homologous recombination by the Latour method 657.3 Kb (5.43%) Decreased uptake of glucose and some amino acids compared with the parental strain 2.7-fold increase in the concentration of cellular adenosine triphosphate; 1.7- and 1.8-fold increase in the production of green fluorescent protein and secreted human growth hormone, respectively 13