Table 2.

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

Method	Targeted cellular component	Target organism	Engineered phenotype	References
Global transcription machinery engineering (gTME)	General sigma factor σ70, stationary phase sigma factor σS, 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]