Protease-resistant systems for polypeptide display and methods of making and using thereof
The present invention generally relates to bacterial polypeptide display systems, libraries using these bacterial display systems, and methods of making and using these systems, including methods for improved display of polypeptides on the extracellular surface of bacteria using circularly permuted transmembrane bacterial polypeptides that have been modified to increase resistance to protease degradation and to enhance polypeptide display characteristics.
1. A composition comprising:
a carrier polypeptide (CP) comprising at least a transmembrane polypeptide portion, wherein the CP comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 56 and SEQ ID NO: 57, and
a displayed moiety (DM)
wherein the CP and the DM are operably linked.
2. The composition of claim 1 , wherein the DM is displayed on the N-terminus of the CP.
3. The composition of claim 1 , wherein the DM is displayed on the C-terminus of the CP.
4. The composition of claim 1 , wherein the CP comprises
the amino acid sequence of SEQ ID NO: 1,
an amino acid sequence selected from the group consisting of GQSGQ (SEQ ID NO: 7), GGSGQSGQGG (SEQ ID NO: 9), GGSGQSGQ (SEQ ID NO: 22), GGSGQSGQGS (SEQ ID NO: 59), GGSG (SEQ ID NO: 15), GGSGGSGGSGGSG (SEQ ID NO: 20), and GSSGGQGGSGGSGGSGGSGGSA (SEQ ID NO: 11) N-terminal to the amino acid sequence of SEQ ID NO: 1, and
an amino acid sequence selected from the group consisting of GGS (SEQ ID NO: 17), GGSGGSSGQAAAG (SEQ ID NO: 12), and GGSGGSSGQTAAG (SEQ ID NO: 83) C-terminal to the amino acid sequence of SEQ ID NO: 1.
5. The composition of claim 1 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 4 or SEQ ID NO: 58.
6. The composition of claim 1 , wherein the CP is operably linked to the DM to form a display platform (DP) having the structural arrangement from N-terminus to C-terminus: CP-DM or DM-CP, wherein the DP comprises an N-terminus tag, a C-terminus tag or both an N-terminus tag and a C-terminus tag.
7. The composition of claim 6 , wherein the DP comprises both an N-terminus tag and a C-terminus tag.
8. The composition of claim 7 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 1, and wherein:
(i) the N-terminal tag comprises an amino acid sequence selected from the group consisting of GQSGQ (SEQ ID NO: 7), GGSGQSGQGG (SEQ ID NO: 9), GGSGQSGQ (SEQ ID NO: 22), GGSGQSGQGS (SEQ ID NO: 59), GGSG (SEQ ID NO: 15), GGSGGSGGSGGSG (SEQ ID NO: 20), and GSSGGQGGSGGSGGSGGSGGSA (SEQ ID NO: 11); or
(ii) the C-terminal tag comprises an amino acid sequence selected from the group consisting of GGS (SEQ ID NO: 17), GGSGGSSGQAAAG (SEQ ID NO: 12), and GGSGGSSGQTAAG (SEQ ID NO: 83); or
(iii) the N-terminal tag comprises an amino acid sequence selected from the group consisting of GQSGQ (SEQ ID NO: 7), GGSGQSGQGG (SEQ ID NO: 9), GGSGQSGQ (SEQ ID NO: 22), GGSGQSGQGS (SEQ ID NO: 59), GGSG (SEQ ID NO: 15), GGSGGSGGSGGSG (SEQ ID NO: 20), and GSSGGQGGSGGSGGSGGSGGSA (SEQ ID NO: 11) and the C-terminal tag comprises sequence an amino acid sequence selected from the group consisting of GGS (SEQ ID NO: 17), GGSGGSSGQAAAG (SEQ ID NO: 12), and GGSGGSSGQTAAG (SEQ ID NO: 83).
9. The composition of claim 7 , wherein N-terminal tag comprises the amino acid sequence EYMPME (SEQ ID NO: 8).
10. The composition of claim 7 , wherein the C-terminal tag comprises a histidine tag.
11. The composition of claim 10 , wherein the histidine tag is an 8-His tag.
12. The composition of claim 7 , wherein the N-terminal tag comprises the amino acid sequence EYMPME (SEQ ID NO: 8) and the C-terminal tag comprises an 8-His tag.
13. The composition of claim 7 , wherein the DP comprises more than one DM.
14. The composition of claim 13 , wherein the DP has the structural arrangement from N-terminus to C-terminus: T1-DM1-DM2-CP-T2, T1-CP-DM1-DM2-T2, T1-DM1-DM2-DM3-CP-T2, T1-CP-DM1-DM2-DM3-T2, or T1-DM1-CP-DM2-T2.
15. The composition of claim 1 , wherein the composition comprises one or more linkers.
16. The composition of claim 6 , wherein the DP comprises one or more linkers.
17. The composition of claim 1 , wherein the DM is selected from the group consisting of a substrate, an exosite, a masking moiety, an antibody, a receptor, a ligand, and other proteins, and any combinations thereof.
18. The composition of claim 17 , wherein the substrate is a substrate for a protease.
19. A composition comprising: a replicable biological entity; and a displayed moiety (DM) displayed on the surface of the replicable biological entity, wherein the DM is fused to an extracellular terminus of a circularly permuted bacterial outer membrane carrier protein (CP) to produce a display platform (DP), wherein the CP comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 56 and SEQ ID NO: 57.
20. The composition of claim 19 , wherein the DM is a substrate for an enzyme.
21. The composition of claim 19 , wherein the DP comprises a tag.
22. The composition of claim 21 , wherein the tag is a fluorescent agent.
23. The composition of claim 21 , wherein the tag is a C-terminal tag.
24. The composition of claim 21 , wherein the tag is an N-terminal tag.
25. The composition of claim 19 , wherein the C-terminus of the CP is exposed on the surface of the replicable biological entity.
26. The composition of claim 19 , wherein the N-terminus of the CP is exposed on the surface of the replicable biological entity.
27. The composition of claim 19 , wherein the replicable biological entity is a bacterial cell.
28. A peptide display scaffold, comprising a fusion protein comprising a formula selected from the group consisting of:
[T1-DM]-carrier protein-[T2] and(2)[T1]-carrier protein-[DM-1-T2] (1)
wherein
the carrier protein is a circularly permuted bacterial outer membrane protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 56 and SEQ ID NO: 57;
DM comprises a candidate peptide; and
T1 and T2 are first and second detectable moieties;
and wherein, when the fusion protein is expressed in a cell comprising a cell outer membrane, T1-DM and T2 in formula (1) or T1 and DM-T2 in formula (2) are exposed at an extracellular surface of the cell outer membrane and one or both of the N- and C-termini of the fusion protein are exposed at the extracellular surface of the cell outer membrane.
29. The composition of claim 1 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 1.
30. The composition of claim 1 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 56.
31. The composition of claim 1 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 57.
32. The composition of claim 19 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 1.
33. The composition of claim 19 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 56.
34. The composition of claim 19 , wherein the CP comprises the amino acid sequence of SEQ ID NO: 57.
35. The composition of claim 28 , wherein the carrier protein comprises the amino acid sequence of SEQ ID NO: 1.
36. The composition of claim 28 , wherein the carrier protein comprises the amino acid sequence of SEQ ID NO: 56.
37. The composition of claim 28 , wherein the carrier protein comprises the amino acid sequence of SEQ ID NO: 57.