Yeast cell surface display of proteins and uses thereof

• US 6,699,658 B1
• Filed: 01/20/1998
• Issued: 03/02/2004
• Est. Priority Date: 05/31/1996
• Status: Expired due to Term

• Current Assignee: National Institutes of Health (NIH) (Government of the United States of America)
• Original Assignee: Board of Trustees of The University of Illinois
• Inventors: Kranz, David M., Wittrup, K. Dane, Boder, Eric T., Kieke, Michele
• Primary Examiner(s): Guzo, David
• Application Number:
  US09/009,388
• Time in Patent Office: 2,233 Days
• Field of Search: 435/4, 435/6, 435/7.1, 435/7.2, 435/7.31, 435/69.1, 435/172.1, 435/172.3, 435/320.1, 435/252.3, 435/254.1, 435/254.11, 435/254.2, 435/254.21, 435/254.23
• US Class Current: 435/6.14
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C40B 40/02 Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
• CPC Class Codes: G01N 2333/39 from yeasts
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/6854 Immunoglobulins

Abstract

The present invention provides a genetic method for tethering polypeptides to the yeast cell wall in a form accessible for binding to macromolecules. Combining this method with fluorescence-activated cell sorting provides a means of selecting proteins with increased or decreased affinity for another molecule, altered specificity, or conditional binding. Also provided is a method for genetic fusion of the N terminus of a polypeptide of interest to the C-terminus of the yeast Aga2p cell wall protein. The outer wall of each yeast cell can display approximately 10⁴ protein agglutinins. The native agglutinins serve as specific adhesion contacts to fuse yeast cells of opposite mating type during mating. In effect, yeast has evolved a platform for protein-protein binding without steric hindrance, from cell wall components. As one embodiment, attaching an scFv antibody fragment to the Aga2p agglutinin effectively mimics the cell surface display of antibodies by B cells in the immune system for affinity maturation in vivo. As another embodiment, T cell receptor mutants can be isolated by this method that are efficiently displayed on the yeast cell surface, providing a means of altering T cell receptor binding affinity and specificity by library screening.

Claims

1. A method for selecting proteins for displayability on a yeast cell surface, comprising:

transforming yeast cells with a vector which expresses a protein to be tested fused to a yeast cell wall protein, wherein mutagenesis is used to generate a variegated population of mutants of the protein to be tested;

contacting said yeast cells with a label which binds to proteins that are displayed on the yeast cell surface and does not bind to proteins that are not displayed on the yeast cell surface;

isolating said yeast cells with which said label is bound, wherein the presence of said label bound to a protein to be tested indicates said protein to be tested is displayable on the yeast cell surface.

3. The method of claim 1, wherein said protein to be tested is the T cell receptor.

5. The method of claim 1, wherein said protein to be tested is an antibody, Fab, Fv, or scFv antibody fragment.

6. The method of claim 1, wherein said protein to be tested is the ligand binding domain of a cell surface receptor.

7. The method of claim 6, wherein said cell surface receptor is a T cell receptor.

8. The method of claim 3, wherein said protein to be tested is a single-chain T cell receptor.

2. A method for selecting proteins for displayability on a yeast cell surface, comprising:

transforming yeast cells with a vector which expresses a protein to be tested fused to a yeast cell wall protein, wherein mutagenesis is used to generate a variegated population of mutants of the protein to be tested;

contacting said yeast cells with a label which binds to proteins that are displayed on the yeast cell surface and does not bind to proteins that are not displayed on the yeast cell surface;

isolating said yeast cells with which said label is bound, wherein the presence of said label bound to a protein to be tested indicates said protein to be tested is displayable on the yeast cell surface, wherein the label is selected from the group consisting of;

KJ16 and IB2.

4. A method for selecting proteins for displayability on a yeast cell surface, comprising:

transforming yeast cells with a vector which expresses a protein to be tested fused to a yeast cell wall protein, wherein mutagenesis is used to generate a variegated population of mutants of the protein to be tested;

contacting said yeast cells with a label which binds to proteins that are displayed on the yeast cell surface and does not bind to proteins that are not displayed on the yeast cell surface;

isolating said yeast cells with which said label is bound, wherein the presence of said label bound to a protein to be tested indicates said protein to be tested is displayable on the yeast cell surface, wherein said protein to be tested is scFv-KJ16 and said label is a T cell.

9. A method for selecting proteins with improved binding to a label comprising:

transforming yeast cells with a vector expressing a protein to be tested fused to a yeast cell wall protein;

contacting said yeast cells with a first label which binds to said protein to be tested;

determining the level of said first label, wherein a higher level of said label indicates the protein to be tested has improved binding to the label than a protein to be tested that exhibits a lower level of said label.

10. The method of claim 9, further including the steps of:

labeling said yeast cells with a second label, wherein said vector used to transform said yeast cells contains means for expressing a polypeptide sequence fused to said protein to be tested to produce a fusion polypeptide and said second label associates with yeast cells expressing said fusion polypeptide and does not associate with yeast cells which do not express said fusion polypeptide;

enriching a transformed yeast population by quantitating said second label, wherein an occurrence of said second label is directly proportional to an abundance of said fusion polypeptides expressed on the cell surface; and

comparing said quantitation of said first label to said quantitation of said second label to determine relative binding of said first label to said protein to be tested.

11. The method of claim 9, wherein said yeast cell wall protein becomes covalently attached to the cell by disulfide bonds during expression.

12. The method of claim 9, wherein the yeast cell wall protein is an agglutinin.

13. The method of claim 9, wherein the yeast cell wall protein is the binding subunit of an agglutinin.

14. The method of claim 9, wherein the yeast cell wall protein is Aga2p.

15. The method of claim 9, wherein the protein to be tested is fused by its N terminus to the C terminus of a binding subunit of an agglutinin.

16. The method of claim 9, wherein the protein to be tested is fused by its N terminus to the C terminus of Aga2p.

17. The method of claim 9, wherein said yeast cell is of a genus selected from the group consisting of Saccharomyces, Pichia, Hansenula, Schizosaccharomyces, Kluyveromyces, Yarrowia, and Candida.

18. The method of claim 9, wherein said first label is a magnetic particle attached to a ligand for the protein to be tested.

19. The method of claim 9, wherein said protein to be tested is an antibody, Fab, Fv, or scFv antibody fragment.

20. The method of claim 9, wherein said protein to be tested is the ligand binding domain of a cell surface receptor.

21. The method of claim 9, wherein said protein to be tested is a soluble ligand of a cell surface receptor.

22. A vector for performing the method of claim 9, comprising a gene coding for said cell wall protein fused to a gene for said protein of interest.

23. The method of claim 9, wherein expression of the fusion protein is controlled by an inducible promoter.

24. The method of claim 10, wherein said polypeptide portion of said fusion polypeptide recognized by said second label is an epitope tag.

25. The method of claim 10, wherein said first label and said second label are fluorescent labels.

26. The method of claim 10, wherein mutagenesis is used to a generate a variegated population of mutants of the protein to be tested.

27. The method of claim 14, wherein Aga2p expression is controlled by the GAL 1-10 promoter.

28. The method of claim 17, wherein said yeast cell is of the species Saccharomyces cerevisiae.

29. The method of claim 24, wherein the epitope tag is c-myc or HA.

30. The method of claim 25, wherein said quantitation and enrichment steps are performed by fluorescent flow cytometry.

31. The method of claim 25, wherein said quantitation and enrichment steps are performed by fluorescence microscopy.

32. The method of claim 26, wherein mutagenesis is performed by randomly mutating said vector by passage in a mutator bacterial strain which performs error-prone DNA replication.

33. The method of claim 26, wherein mutagenesis is performed by site directed mutagenesis of specific amino acid residues of said protein to be tested.

34. The method of claim 26, wherein selection of mutated proteins of interest with improved binding properties involves iterative cycles of said quantitating and labeling steps.

35. The vector of claim 22, further comprising a nucleic acid encoding an epitope tag polypeptide fused to said gene for said protein of interest.

36. The vector of claim 22, wherein said cell wall protein is an agglutinin.

37. The vector of claim 22, wherein said cell wall protein is the binding subunit of an agglutinin.

38. The vector of claim 22, wherein said yeast agglutinin is Aga2p.

42. The method of claim 23, wherein the inducible promoter is the GAL 1-10 promoter.

39. A vector for performing the method for selecting proteins with improved binding to a label, said method comprising:

transforming yeast cells with a vector expressing a protein to be tested fused to a yeast cell wall protein;

contacting said yeast cells with a first label which binds to said protein to be tested;

determining the level of said first label, wherein a higher level of said label indicates the protein to be tested has improved binding to the label than a protein to be tested that exhibits a lower level of said label said, vector comprising a gene coding for said cell wall protein fused to a gene for said protein of interest, wherein a flexible unstructured polypeptide linker is fused between the cell wall protein and the protein of interest.

41. The vector of claim 39, wherein the said flexible polypeptide linker has the sequence GGGGSGGGGSGGGGS (SEQ ID NO. 20).

40. A vector for performing the method for selecting proteins with improved binding to a label, said method comprising:

transforming yeast cells with a vector expressing a protein to be tested fused to a yeast cell wall protein;

contacting said yeast cells with a first label which binds to said protein to be tested;

determining the level of said first label, wherein a higher level of said label indicates the protein to be tested has improved binding to the label than a protein to be tested that exhibits a lower level of said label, said vector comprising a gene coding for said cell wall protein fused to a gene for said protein of interest, further comprising a nucleic acid encoding an epitope tag polypeptide fused to said gene for said protein of interest, wherein said epitope tag polypeptide is selected from the group of HA (SEQ ID NO.

     1), or c-myc (SEQ ID NO.

     2), or a sequence selected from the group of DTYRYI (SEQ ID NO.

     3), TDFYLK (SEQ ID NO.

     4), EEEEYMPME (SEQ ID NO.

     5), KPPTPPPEPET (SEQ ID NO.

     6), HHHHHH (SEQ ID NO.

     7), RYIRS (SEQ ID NO.

     8), and DYKDDDDK (SEQ ID NO.

     9).