Table 2 Representative genome engineering strategies which could be applied to the enhancement of recombinant protein production in bacteria

Global transcription machinery engineering (gTME)

General sigma factor σ⁷⁰, stationary phase sigma factor σ^S, RNA polymerase a subunit

E. coli

Ethanol, butanol, isobutanol, pentanol, and 3-pentanol tolerance; lycopene, L-tyrosine, and hyaluronic acid production

[55, 66, 68]

Transcription factor Spt15p

S. cerevisiae

Ethanol tolerance and production

[67]

General sigma factor

Lactobacillus plantarum

lactic acid and hydrochloric acid tolerance

[95]

Libraries of artificial zinc fingers

Zinc fingers

S. cerevisiae

Tolerance to heat and osmotic stress; ketoconazole resistance

[69]

Mouse neuroblastoma cells

Neurogenesis, differentiation of neuroblasts to osteoblasts, proliferation rate

[69]

E. coli

Tolerance to heat, cold, and osmotic stress

[70, 71]

Trackable multiplex recombineering (TRMR)

> 95% of all individual E. coli genes

E. coli

Tolerance to salicin, D-fucose, methylglyoxal, valine, and lignocellulosic hydrolysate

[56]

Genome shuffling

Chromosome

Streptomyces fradiae

Tylosin production

[72]

A strain of Lactobacillus

Tolerance to lactic acid

[73]

Sphingobium chlorophenolicum

Degradation of pentachlorophenol

[74]