In many cases the expressed protein is insoluble and accumulates in so-called inclusion bodies. This is especially true under conditions of high level expression. Several strategies are available to improve the solubility of the expressed protein.

Reducing the rate of protein synthesis.

This can be done by:

  • lowering the growth temperature. This decreases the rate of protein synthesis and usualy more soluble protein is obtained.
  • using a weaker promoter (e.g. trc instead of T7).
  • using a lower copy number plasmid.
  • lowering the inducer concentration.

Changing the growth medium:

  • addition of prosthetic groups or co-factors which are essential for proper folding or for protein stability.
  • addition of buffer to control pH fluctuation in the medium during growth.
  • addition of 1% glucose to repress induction of the lac promoter by lactose, which is present in most rich media (such as LB, 2xYT).
  • addition of polyols (e.g. sorbitol) and sucrose. The increase in osmotic pressure caused by these additions leads to the accumulation of osmoprotectants in the cell, which stabilise the native protein structure.
  • addition of ethanol, low molecular weight thiols and disulfides, and NaCl.
    (Georgiou, G. & Valax, P. (1996) Current Opinion Biotechnol. 7, 190-197)

Co-expression of chaperones and/or foldases.

Two classes of proteins play an important role in in vivo protein folding.

  • Molecular chaperones promote the proper isomerisation and cellular targeting by transiently interacting with folding intermediates. The best characterized E. coli systems are:
    • GroES-GroEL
    • DnaK-DnaJ-GrpE
    • ClpB
  • Foldases accelerate rate-limiting steps along the folding pathway. Three types of foldases play an important role:
    • peptidyl prolyl cis/trans isomerases (PPI's)
    • disulfide oxidoreductase (DsbA) and disulfide isomerase (DsbC)
    • protein disulfide isomerase (PDI) - an eukaryotic protein that catalyzes both protein cysteine oxidation and disulfide bond isomerisation. It also exhibits chaperone activity.

Co-expression of one or more of these proteins with the target protein could lead to higher levels of soluble protein. The levels of co-expression of the different chaperones/foldases have to be optimised for each individual case. DsbA and DsbC have also shown positive effects on expression levels when used as a fusion partner.

Periplasmic expression:

Secretion of the target protein to the periplasm has a number of distinct advantages:

  • the oxidising environment of the periplasm allows for the formation of disulfide bonds, which does not occur in the reducing environment of the cytoplasm.
  • the periplasm contains two foldases, disulfide oxidoreductase (DsbA) and disulfide isomerase (DsbC), that catalyse the formation and isomerisation of disulfide bonds.
  • reduced proteolysis (since less proteins are present).
  • allows for the accumulation of proteins that are toxic in the cytoplasm.
  • engineering of an authentic N-terminus.

Secretion is achieved by the addition of a leader sequence (signal peptide) to the N-terminus of the target protein. Most used leader sequences are pelB and ompT. Unfortunately, expression yield are usually much lower and not all expressed protein is secreted into the periplasm but is also found in the medium, the cytoplasm and the cytoplasmic membrane.

Using specific host strains:

The solubility of disulfide bond containing protein can be increased by using a host strain with a more oxidising cytoplasmic environment. Two strains are commercially available (Novagen):

  • AD494, which has a mutation in thioredoxin reductase (trxB).
  • Origami, a double mutant in thioredoxin reductase (trxB) and glutathione reductase (gor).

Addition of a fusion partner:

Fusion of the N-terminus of a heterologous protein to the C-terminus of a soluble fusion partner often improves the solubility of the fusion protein.

Expression of a fragment of the protein:

E. coli does not express well very large proteins (> 70 kDa). Chosing a smaller fragment of the target protein can improve expression levels and solubility.

The solubility of a poorly soluble (or insoluble) protein can also be improved by selecting only a soluble domain for expression.

In vitro denaturation and refolding of the protein:

When despite all efforts the target protein still is expressed in inclusion bodies, then the last resort is to denature and refold the protein in vitro. This procedure is carried out in three phases:

  • isolation of the inclusion bodies.
  • solubilisation and denaturation of the target protein. This is done by the addition of a denaturing agent (usually guanidine or urea) under reducing conditions (e.g. 20 mM DTT).
  • refolding of the protein by removing the denaturating agent using dialysis, dilution or chromatography. For proteins containing disulfide bonds this has to be carried out in the presence of a redox shuttling system e.g. reduced and oxidised glutathione.

See also: In vitro denaturation and refolding.