Table 1 Top-down genome minimisation projects
From: Trimming the genomic fat: minimising and re-functionalising genomes using synthetic biology
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 |
