Ubiquitin fusion technology represents an emerging method for economic
ally producing peptides and small proteins in the bacterium Escherichi
a coli. Our focus is on peptide production where the need for cost-eff
ective, scaleable processes has recently been highlighted by Kelley (1
996). There are two principal features: (1) the expression system cons
ists of a suitable E. coli host strain paired with a plasmid that enco
des the ubiquitin fusion and (2) an ubiquitin-specific protease, UCH-L
3, which cleaves only C-terminal extensions from ubiquitin. In this wo
rk, multigram yields were obtained of four ubiquitin fusions derived f
rom cell paste generated in single 10-L fermentations. All were expres
sed intracellularly and remained soluble at extremely high levels of e
xpression. Bacterial freeze-thaw lysates contained over 95% pure ubiqu
itin fusion protein. All four fusions were efficiently cleaved to ubiq
uitin and the peptide products. In one case, the final yield of peptid
e was 1.08 g from 3 L of low cell density bacterial culture. The combi
nation of exceptional overexpression of the ubiqutin-peptide fusion pr
oteins and a robust and specific protease are unique advantages contri
buting to a cost-effective, scaleable, and generic bioprocess for pept
ide production.